![]() |
|
| Free
computer
tools in
Structural Bioinformatics and Chemoinformatics |
|
| Table I: Patent search |
|
| Table II: Chemistry toolkits, graphics (small and macro-molecules), other links to bioinformatics and utilities |
|
| Table III: ADME/tox prediction and databases |
|
| Table IV: Free compound collections, target-ligand databases and utilities |
|
| Table V: Small molecules 2D-to-3D, 2D or 3D search and de novo ligand builder |
|
| Table VIa: Receptor 3D structures, homology modeling, structure prediction and macromolecular interaction databases |
|
| Table VIb: Pocket prediction and search for functional regions on targets, analysis of interfaces, Protein docking |
|
| Table VII: Comparison of binding sites/protein functional sites – protein function prediction (see also Table VIb) |
|
| Table VIII: Target analysis: flexibility – energy minimization – normal modes – molecular dynamics –water molecules in target – ions – pKa and electrostatics – point mutations and related utilities |
|
| Table IX: Docking and/or scoring engines for small molecule-macromolecule interactions... Support Vector Machines |
|
| References (they are either in the tables or at the end) |
|
If you have suggestions please contact me
|
Review Current Protein
and Peptide Science, 2007, 8(4):381-411.
Free Resources to Assist Structure-Based Virtual Ligand Screening Experiments B. O. Villoutreix, N. Renault, D. Lagorce, O. Sperandio, M. Montes and M. A. Miteva Get the paper here: (PDF) |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
A project has been initiated to extract chemical information from depictions of molecules in the public literature |
Table II: Chemistry toolkits, graphics (small and macro-molecules), structural bioinformatis, utilities
| URLs | Short summary | Keywords |
| LINK | The web-based RESP ESP charge DataBase is a free and new source of RESP and ESP atomic charge values and force field libraries for model systems and/or small molecules. R.E.DD.B. stores highly effective and reproducible charge values and molecular structures in the Tripos mol2 file format, information about the charge derivation procedure, scripts to integrate the charges and molecular topology in the most common molecular dynamics packages. Moreover, R.E.DD.B. allows users to freely store and distribute RESP or ESP charges and force field libraries to the scientific community, via a web interface. The first version of R.E.DD.B., released in January 2006, contains force field libraries for molecules as well as molecular fragments for standard residues and their analogs (amino acids, monosaccharides, nucleotides and ligands), hence covering a vast area of relevant biological applications. Francois-Yves Dupradeau, Christine Cezard, Rodolphe Lelong, elodie Stanislawiak, Julien Pecher, Jean Charles Delepine, and Piotr Cieplak R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries Nucleic Acids Research Advance Access published on October 25, 2007 | Chemistry tools |
| LINK | AtomEye: atomistic configuration viewer. AtomEye analyse distances and other parameters. In the utilities there, you can find many tools: voronoirize: make nanocrystals with the Voronoi procedure; annotate_atomic_strain: calculate atomic strain tensor; vcut: planar cut using Cartesian-space normal; perturb_x: spatially perturb a configuration; iniT: assign kinetic energy; VASP is a powerful density functional theory (DFT) code. | Chemistry tools |
| LINK | Aten: is a tool for computational chemists, molecular dynamicists. It does: * Build and edit atomic coordinates, either from scratch or from existing configurations, for either isolated molecules or periodic systems (e.g. crystals, surfaces, liquids) * Generate superstructures from crystal information * Easily transform and move coordinates around in 3D * Generate random N-component configurations * Help in the creation of forcefield specificiations for your systems * Write coordinates and forcefield expressions for your systems * Visualise trajectories, glyphs, mapped surfaces, and isosurfaces | Chemistry tools |
| LINK | Jamberoo - cross platform molecular editor | molecular editor |
| LINK | WWW computational chemistry resources | Chemistry tools |
| LINK | Mac Apple Chemistry | Chemistry tools for Apple Mac |
| LINK | The CAMD Open Software project (CAMPOS) is a collection of programs for atomic-scale simulations | Simulation tools |
| LINK | Local move is a Monte-Carlo approach to the problem of finding best-fitting lattice models for biopolymers. Starting from an initial discrete model (3D self-avoiding walk), it performs a sequence of elementary random alterations, called Local Moves. The original atoms coordinate, input as a PDB file, are then used to decide whether or not to accept the candidate move, either deterministically in a greedy way or stochastically by performing a simulated annealing. Through iterating the process for a reasonable amount of time, a model is obtained whose inter-atom distance is very close to the original model. Y. Ponty, R. Istrate, E. Porcelli, and P. Clote LocalMove: computing on-lattice fits for biopolymers. Nucl. Acids Res. 2008 36: W216-W222; | Simulation tools - Flexibility - Structure Prediction Analysis |
| LINK | Links to the Theoretical and Computational Biophysics group - list of tools essentially for macromolecules | List of tools for macromolecules |
| LINK | List of tools for protein structure analysis | List of tools for protein structural prediction and analysis |
| LINK | List of resources, learning tools in the field of chemoinformatics by Dr. David Wild. You can see his nice introduction: http://chemoinf.com/getting_started/gsic_toc.pdf | List of tools for chemoinformatics and courses |
| LINK | SDFM: An open source molecular database manager in Python, manage SDF files | Free python SDF manager |
| LINK | Links to many computer tools posted by Sung Kwang Lee. Dept. of Chemistry, Yonsei Univ, Korea | Links to computer tools |
| LINK | QSAR World is a free online resource for QSAR & modeling professionals that provides comprehensive information on technical aspects, makes manually curated datasets available freely and provides listing of many major other resources along with detailed technical articles and features written by reputed scientists | Free online resource for QSAR & modeling professionals |
| LINK | Links to cheminformatics programs and QSAR datasets. These include, diversity and similarity searches. Many compounds designed for specific targets (e.g., coagulation factor Xa...) | Compound searching |
| LINK | Links to many computer tools | Modeling tool links |
| LINK | World wide molecular matrix, provide several services, including OpenBabel online |
Chemistry tools |
| LINK | Experimental Data Checker and OSCAR Toolkit. Experimental data on new molecules in organic and inorganic chemistry is presented in a standard form which varies little from journal to journal. Typically, the appearance of the compound is described, followed by melting points (if applicable), Rf, infra-red and NMR data, and mass spectral information. Java toolkit is available which will extract this information from either a paragraph of experimental data, or a full paper, and then run some checks to test the data for consistency. It consists of an application for authors and editors to use to check their data before publication, along with the toolkit which can be used to develop other applications are freely available on this site. | Chemistry tools - Search Patents - Fetch chemical |
| LINK | Mol2 file format (2D or 3D) |
Mol2 format (Chemistry) |
| LINK | The Protein Data Bank, see section describing the PDB format (Deshpande et al. 2005) |
Macro-molecule 3D structures |
| LINK | Information about different chemical structure file formats including SDF. (Dalby et al. J. Chem. Inf. Comput. Sci, 32, 244-255, 1992) | Chemistry tools |
| OpenBabel: File format conversion | Chemistry tools | |
| LINK | FAF-Drugs: OpenBabel online (Miteva et al. 2006) | Chemistry tools |
| LINK | Chemistry blog | Chemistry blog |
| LINK | C-ChemBench: The Carolina Cheminformatics Workbench (C-ChemBench) is an integrated toolkit developed by the Carolina Exploratory Center for Cheminformatics Research (CECCR) with the support of the National Institutes of Health | Chemistry tools |
| LINK | iBabel: File format conversion and other chemistry tools (essentially for Mac or Linux/Unix) | Chemistry tools |
| LINK | Tutorial for SMILES and chemistry toolkit | SMILES format (Chemistry) |
| LINK | MMFF validation suite | Simulation tools |
| LINK | Chemistry toolkit | Chemistry tools |
| LINK | IUPAC International Chemical Identifier project | Chemistry tools |
| LINK | GIF/PNG-creator with SMILES input | Compound drawing |
| Computational chemistry package | Chemistry tools | |
| LINK | Computational chemistry package (Hassinen and Perakyla 2001). Unfortunately, can be very very tuff to compile, so far always rpm missing for us!! | Chemistry tools |
| LINK | JME: Java Molecular Editor by Dr. P. Erlt, draws small molecules and get SMILES | Compound drawing, Get SMILES |
| LINK | Computer tools for chemistry, ADME-tox....Marvin is a suite of Java based chemistry software that have different forms: Marvin Applets, Marvin Beans, MarvinSketch | Chemistry tools |
| LINK | CDK: Chemistry development kit (Steinbeck et al. 2006) | Chemistry tools |
| LINK | Chemistry toolkit | Chemistry tools |
| LINK | A C++ toolbox for chemoinformatics (Mahe et al. 2005) | Chemistry tools |
| LINK | SketchEI: Chemical structure sketching tool | Compound drawing |
| LINK | Online SMILES translator and structure generator from F. Oellien and M.C. Nicklaus | Compound drawing |
| LINK | The SDF toolkit (in Perl) essentially for small molecules | Chemistry tools |
| LINK | To display and rotate macromolecules and small molecules in a single internet browser | Molecular graphics |
| LINK | MOLMOL (Koradi et al. 1996): molecular graphics program for the structure of biological macromolecules | Molecular graphics |
| LINK | Cn3D (Hogue, 1997): displays structures of macromolecules and performs sequence alignments | Molecular graphics |
| LINK | DINO : 3D viewer essentially for macromolecules | Molecular graphics |
| LINK | DisMol: Java applet viewer for macromolecules and small molecules | Molecular graphics |
| MolScript: creates molecular graphics image of macromolecules and small molecules (Kraulis 1991) | Molecular graphics | |
| LINK | Colorado3D (Sasin and Bujnicki 2004): web server for the visual analysis of protein structures | Molecular graphics, Structural analysis |
| LINK | Pymol : molecular graphics system to look at macromolecules and small molecules | Molecular graphics, structural analysis |
| LINK | VMD (Humphrey et al. 1996): molecular visualization program for displaying, animating, and analyzing large systems | Molecular graphics, structural analysis |
| LINK | MolWorks: graphic tool for drawing and sketching molecules | Chemistry tools |
| LINK | ChemSpotlight: metadata importer pluging for Mac OS X, which reads common chemical file formats (PDB, Mol2, SDF...) | Chemistry tools |
| LINK | DRAWNA (Massire et al. 1994): program for drawing schematic views of nucleic acids | Molecular graphics |
| LINK | ICM browser (Abagyan et al. 1994): biomolecular modeling package (can read many different file formats) | Molecular graphics |
| LINK | OpenEye Vida : molecular modeling package for macromolecules and small molecules (can read many different file formats) | Molecular graphics |
| LINK | PovChem is a chemical visualization and illustration program, it can calculate and display hydrogen bonds | Molecular graphics, structural analysis |
| LINK | With gOpenMol allows visualization and analysis of small molecules, and to lesser extent protein structures, of chemical properties, total electron densities and molecule orbitals (Laaksonen 1992) | Molecular graphics |
| LINK | KMovisto is a 3D molecule viewer essentially for Linux. It can import and export OpenBabel files | Molecular graphics |
| LINK | YASARA is a molecular-graphics, -modeling and -simulation program (Krieger et al. 2002; Krieger et al. 2006) | Molecular graphics and modeling |
| GDIS is a program for the display and manipulation of isolated molecules and periodic systems | Molecular graphics | |
| KDrawChem and XDrawChem are molecular structure drawing programs | Compound drawing | |
| LINK | BKchem is a chemical drawing program | Compound drawing |
| LINK | Many tools for modeling and mining small molecules, proteins, DNA, RNA, partial charges...solvent accessible molecular surface area with MASKER... | Molecular modeling |
| LINK | UCSF Chimera (Pettersen et al. 2004): biomolecular modeling package. Can be used for small and large molecules, many tools for active site analysis, check H-bonds, fit into EM data... | Molecular graphics and modeling |
| LINK | Tautomer generator is a program that generates a set of molecules (tautomers) from a molecular core and number of hydrogen atoms | Simulation tools |
| LINK | Moloc: Roche Biostructural modeling package for small and large molecules. This package seems free but ? | Chemistry tools |
| LINK | Open source molecule viewer | Molecular graphics |
| LINK | JChemPaint is a program for drawing 2D chemical structures | Compound drawing |
| LINK | MayaChemTools is a growing collection of Perl scripts to support day-to-day computational discovery needs. Now on May 2008, the new release has fingerprints, similarities... | Chemistry tools |
| LINK | A Java Chemical Structure Editor (Trepalin et al. 2006) | Compound drawing |
| LINK | Links to protein crystallography tools such as CCP4, etc | Molecular graphics and modeling, many valuable links |
| LINK | Links to Free Molecular Visualization and Modeling Software. World Index of BioMolecular Visualization Resources | Molecular graphics and modeling, many valuable links, but packages may not be free |
| LINK | Bioclipse is a Java-based visual platform for chemo- and bioinformatics | Molecular graphics |
| LINK | Information about SDF format | SDF format |
| LINK | DeepView, the Swiss-PDBViewer | Graphics, Molecular Modeling |
| LINK LINK |
FirstGlance in Jmol, a simple tool for macromolecular visualization (installed online at these sites) | Graphics, Molecular Modeling |
| LINK | jAMVLE: jmol Amalgamated Molecular Visualization Learning Environment | Graphics |
| LINK | Publications in bioinformatics | Publications Bioinfo |
| LINK | Compilation of Molecular Biology Web: web servers, free packages... | Numerous links to structural bioinformatics tools |
| LINK | SeqAlert(c) is a sequence alerting service that will periodically compare your sequence(s) against sequences from determined 3D structures, or structures being determined ... | Information about the 3d structure you are waiting for |
| LINK | Publications in bioinformatics | Publications Bioinfo |
| LINK | Vigyaan is an electronic workbench for bioinformatics, computational biology and computational chemistry. It has been designed to meet the needs of both beginners and experts. VigyaanCD is a live Linux CD containing all the required software to boot the computer with ready to use modeling software. VigyaanCD v1.0 is based on KNOPPIX v3.7. Note: Users do not need to change anything on their hard disk (and do not need to install Linux) to use VigyaanCD. | Different modeling packages |
| LINK | Molecular graphics | Molecular graphics |
| LINK | The PSI3 suite of quantum chemical programs is designed for efficient, high-accuracy calculations of properties of small to medium-sized molecules. The package's current capabilities include a variety of Hartree-Fock, coupled cluster, complete-active-space self-consistent-field, and multi-reference configuration interaction models. Molecular point-group symmetry is utilized throughout to maximize efficiency. The latest version of the code, PSI 3.2, rests upon a completely rewritten infrastructure relative to previous versions of the package. Non-standard computations are possible using a customizable input format. | ab initio quantum chemistry package |
| LINK | Numerous links to software, databases... | QSAR and Modelling society, numerous links |
| LINK | MOPAC (Molecular Orbital PACkage) is a semiempirical quantum chemistry program based on Dewar and Thiel's NDDO approximation. MOPAC2007 does a lot including predicting pKa directly. It is very fast (and it's free for academics). The methodology is based on O-H bond length and partial charge from PM6 and COSMO calculations. The 109 examples listed give an average unsigned error of 0.31 log units | semiempirical quantum chemistry - ADME since pKa |
| LINK | Numerous info about chemoinformatics | chemoinformatics data |
| LINK | Numerous links for chemistry and computer tools | Many chemistry links by Dr. L P Taylor |
| LINK | Protein movie generator | Make movie for your molecule |
| LINK | Walking the web of chemical informatics, package like Ruby CDK chemistry toolkit | Ruby CDK chemistry toolkit and many others |
| LINK | An open source workbench for chemo- and bioinformatics built on the Eclipse Rich Client Platform (RCP) | chemo- and bioinformatics |
| LINK | ChemFileBrowser is a win32 free sotfware for chemistry | Some Chemistry tools for windows |
| LINK | Many links to computer packages from the International Centre for Science and high Technology | Many links to free packages |
| LINK | Many tools from Andrew C.R. Martin's Bioinformatics group. From mutations to Profit for rmsd computations to sending jobs to cluster | Many valuable tools for structural bioinformatics |
| LINK | Prof Alexandre VARNEK web site - links to many French groups in Chemoinformatics | Alexandre VARNEK web site |
| LINK | Software list from the QSAR and Modelling society | Software list |
| LINK | software, shareware and freeware for Macintosh, Windows and Palm | for mac and windows |
| LINK | sourceforge.net chemistry and bioinformatics | sourceforge.net |
| LINK | Obviously Linux for Chemistry | Linux for Chemistry |
| URLs | Short summary | Keywords |
| LINK | chemxseer is an integrated digital library and database allowing for intelligent search of documents in the chemistry domain and data obtained from chemical kinetics | Chemical Database Compound Search ADME |
| LINK | Roadrunner is a chemical database application developed and supported by the Informatics Core of the New Mexico Molecular Libraries Screening Center at the University of New Mexico Health Sciences Center. The wiki explaining the structure of the database is: http://poblano.health.unm.edu/rrwiki/index.php/Developer_Docs | Chemical Database Compound Search ADME |
| LINK | OSIRIS Property Explorer | Physical Property Estimation ADME |
| LINK | Physical Property Estimation | Physical Property Estimation ADME |
| LINK | PK/DB is a free database and predictive service for researches. The main goals are to develop and offer effective prediction models for important pharmacokinetic (PK) properties, such as absorption, distribution, metabolism and excretion (ADME). Therein scientists can find drugs, drug-like, new chemical entities (NCE) among several others measured compounds, in a total of 1303 entries, with their respective PK properties. PK/DB allows users to draw a chemical compound and to search PK data for chemicals similar or identical to the query compound. The highly diverse compounds of the database belong to a variety of therapeutic classes, including antiviral, antibacterial, anti-inflammatory, antipsychotic, antifungal, antihypertensive, antidepressant, immunosuppressive, analgesic, antineoplastic and antilipemic, among several others. As a cheminformatic tool PK/DB offers in silico models where it is possible predict approximate PK properties for promising compounds. Other useful tool that PK/DB provides is based on MarvinSketch applet program where is possible: draw, visualize, edit and save structures in different formats. | ADME/tox |
| LINK | Toxtree Toxtree is a flexible user-friendly application for grouping chemicals and for predicting various types of toxicity based on decision tree approaches. Version 1.20 incorporates the Cramer classification scheme, the Verhaar scheme and rules for predicting skin irritation and corrosion. | ADME/tox, european REACH... |
| LINK | lazar (Lazy Structure-Activity Relationships) is a tool for the prediction of toxic activities of chemical structures. lazar derives predictions from databases with experimental toxicity data. It searches in these databases for compounds with similar structures and calculates the prediction from their measured activities. Free access to lazar predictions. Please do not submit confidential information, because it travels unencrypted over the net. You can obtain predictions for confidential structures and further toxicity endpoints from www.in-silico.de. If you use lazar for scientific work, you should cite C. Helma: Lazy Structure-Activity Relationships (lazar) for the Prediction of Rodent Carcinogenicity and Salmonella Mutagenicity., Molecular Diversity 10, 147-158 (2006). | ADME/tox, rodent carcinogenicity... |
| LINK | Cancer expert system, carcinogenicity... | ADME/tox, carcinogenicity... |
| LINK | The VirtualToxLab, software, soon web page...the Biographics Lab 3R is a non-profit research organization dedicated to the reduction and replacement of animal testing by computational methods. | ADME/tox, carcinogenicity... |
| LINK | AlogP: Tools to predict logP (with several methods) (Tetko and Tanchuk 2002) | ADME/tox |
| LINK | ZINC (Irwin and Shoichet 2005): ADME/tox online | ADME/tox |
| LINK | Chemistry Databases on the Web -- alphabetical list -- and many more ADME tox... | Chemistry Databases, ADME tox... on the Web |
| LINK | Find compound properties | Chemistry |
| LINK | ADME/tox based on CDK (Steinbeck et al. 2006) | ADME-tox |
| LINK | ADME/tox computations | ADME/tox |
| LINK | ADME/tox online | ADME/tox |
| LINK | ADME/tox online | ADME/tox |
| LINK | ADME/tox online | ADME/tox |
| LINK | ADME/tox | ADME/tox |
| LINK | ADME/tox online | ADME/tox |
| LINK | Checkmol is a command-line utility program which reads molecular structure files in different formats (see below) and analyzes the input molecule for the presence of various functional groups and structural elements. At present, approx. 200 different functional groups are recognized. Output can be either clear text (English or German), a bitstring or its ASCII representation, or a set of special 8-character codes. This output can be easily placed into a database table, permitting the creation of chemical databases with a functional group search option. Here is a complete list of recognized function groups (PDF). Another output option of checkmol is a set of statistical values derived from a given molecule, which can also be used for quick retrieval from a database. These values include: the number of atoms, bonds, and rings, the number of differently hybridized carbon, oxgen, and nitrogen atoms, the number of C=O double bonds, the number of rings of different sizes, the number of rings containing nitrogen, oxygen, sulfur, the number of aromatic rings, the number of heterocyclic rings, etc. The combination of all of these values for a given molecule represents some kind of "fingerprint" which is useful for rapid pre-selection in a database structure/substructure search prior to a full atom-by-atom match (see below). For a fully functional set of PHP scripts implementing such a web database (plus utility scripts for data import), please visit the MolDB4 homepage. Matchmol complements the capabilities of checkmol. It compares two (or more) molecular structures and determines whether one of them is a substructure of the other one. This is done by a full atom-by-atom comparison of the input structures. Thus, matchmol can be used as a back-end program for structure/substructure search operations in chemical databases. | Find chemical groups - parse molecules |
| LINK | LEVER (chemical library editing, visualizing and enumerating resource) is a platform-independent tool that not only enumerates chemical libraries using customized fragments, but also computes the physicochemical properties of the generated compounds along with filtering functionalities for evaluating their drug-likeness | ADME/tox Database |
| LINK | FAF-Drugs: ADME/tox online (Miteva et al. 2006) | ADME/tox |
| LINK | XLOGP3: Compute logP. Cheng et al. "Computation of Octanol-Water Partition Coefficients by Guiding an Additive Model with Knowledge", J. Chem. Inf. Model. 2007, 47, 2140-2148 | ADME/tox |
| LINK | Compute logP, retrieves experimental logP for over 13,000 compounds | ADME/tox |
| LINK | DBFILTER can check the mol2 format of compounds in a database and pick out problematic structures for the docking package DOCK. It can also compute ADME/tox properties (12 kinds of filters) | ADME/tox. COMMENTS: The link is broken, i can not find the new one, Dec 2, 2006 |
| LINK | Xscore: logP computation tool (Wang et al. 2000a) | ADME/tox |
| LINK | Compute logP | ADME/tox |
| LINK | PHYSPROP database, contains chemical structures, names and physical properties for over 25,000 compounds | Chemistry database |
| LINK | This database, which is maintained by the National Magnetic Resonance Facility at Madison, is a resource for metabolomics research based on nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) | Metabolomics |
| LINK | The MetaSite has been developed to predict the site of metabolism (i.e., the place in a molecule where the metabolic reaction occurs) for substrates of 2C9, 2D6, 3A4, 1A2 and 2C19 cytochromes (Cruciani et al. 2005) | ADME/tox |
| LINK | logP prediction | ADME/tox |
| LINK | Artificial neural network based approach, using atomic fragmental descriptors, to predict logP on a wide range of organic compounds and other ADME/tox tools (Demo) | ADME/tox |
| LINK | PharmGKB is a knowledge base that captures the relationships between drugs, diseases/phenotypes and genes involved in pharmacokinetics (PK) and pharmacodynamics (PD). This information includes literature annotations, primary data sets, PK and PD pathways, and expert-generated summaries of PK/PD relationships between drugs, diseases/phenotypes and genes. PharmGKB's website is designed to effectively disseminate knowledge to meet the needs of our users. PharmGKB currently has literature annotations documenting the relationship of over 500 drugs, 450 diseases and 600 variant genes. In order to meet the needs of whole genome studies, PharmGKB has added new functionalities, including browsing the variant display by chromosome and cytogenetic locations, allowing the user to view variants not located within a gene. We have developed new infrastructure for handling whole genome data, including increased methods for quality control and tools for comparison across other data sources, such as dbSNP, JSNP and HapMap data. PharmGKB has also added functionality to accept, store, display and query high throughput SNP array data. These changes allow us to capture more structured information on phenotypes for better cataloging and comparison of data. Tina Hernandez-Boussard, Michelle Whirl-Carrillo, Joan M. Hebert, Li Gong, Ryan Owen, Mei Gong, Winston Gor, Feng Liu, Chuong Truong, Ryan Whaley, Mark Woon, Tina Zhou, Russ B. Altman, and Teri E. Klein. The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge. Nucleic Acids Research Advance Access published on November 21, 2007 | ADME/tox; PK/PD |
| LINK | PreADMET is a web-based application for predicting ADME data | ADME/tox |
| LINK | Chemical Effects in Biological Systems (CEBS) knowledge base (application of systems biology to ADME/Tox) | ADME/tox |
| LINK | In order to facilitate drug design, toxic compounds were collected from literature and web sources in the database SuperToxic | ADME/tox database |
| LINK | Toxicoinformatics database at the FDA (application of systems biology to ADME/Tox). See also Leadscope but not free: http://www.leadscope.com/product_info.php?products_id=53 | ADME/tox database |
| LINK | (Thomas et al. 2002): scientific resource for toxicology-related gene expression information (application of systems biology to ADME/Tox) | ADME/tox |
| LINK | cMolP: compute molecular properties | ADME/tox. Jordi Mestres lab, link not working on Dec 2006 |
| LINK | DART (Ji et al. 2003), ADME-AP (Sun et al. 2002), TRMP (Zheng et al. 2004), TTD (Chen et al. 2002a): databases for facilitating the search for drug Absorption, Distribution, Metabolism, Excretion associated proteins. Therapeutic Target Database (268 successful targets in TTD in May 2007) | Databases for ADME/tox, Toxicity |
| LINK | Tissue Distribution DB. TissueDistributionDBs, is a repository of tissue distribution profiles for identifying and ranking the genes in the spectrum of tissue specificity based on Expressed Sequence Tags (ESTs). This repository is currently available for several model organisms across animal and plant kingdoms and is fundamentally based on the UniGene database. | Tissue distribution of several targets |
| LINK | Compumime: tool for the prediction of ADME properties | ADME/tox, COMMENTS: link does not work, Dec 2006 |
| LINK | Biocatalysis/biodegradationdata basees (Ellis et al. 2006): tool for prediction of microbial catabolic reactions involving chemical structures | ADME/tox |
| LINK | MolWorks: many tools including methods for estimating the properties of small molecules | ADME/tox |
| LINK | Distributed Structure-Searchable Toxicity (DSSTox) Database Network (Richard and Williams 2002; Richard et al. 2002). Check also ACToR at http://www.epa.gov/ACToR/ | Databases ADME/tox |
| LINK | Databases on toxicology, hazardous chemicals, environmental health, and toxic releases | Databases ADME/tox |
| LINK | Drug-Induced Toxicity Related Proteins: DITOP | Databases ADME/tox |
Table IV: Free compound collections, target-ligand databases and utilities
| URLs | Short summary | Keywords |
| LINK | Chemical databases | Chemical search |
| LINK | he best B2B directory provides you with enormous chemicals source and trade services of our qualified manufacturers and suppliers catalog. CoreIndex.com provides a fully e-commerce environment in which you can buy, sell and promote your chemicals products and services on-line | Chemical search |
| LINK | Chemical structure lookup search in 39 million indexed structures from 80 databases (27 million unique structures) | Chemical search |
| LINK | ClinicalTrials.gov is a registry of federally and privately supported clinical trials conducted in the United States and around the world. ClinicalTrials.gov gives you information about a trial's purpose, who may participate, locations, and phone numbers for more details. This information should be used in conjunction with advice from health care professionals | Drugs |
| LINK | FDA approved drugs | Drugs |
| LINK | ChemBank: Free collections and utilities, known drugs, many annotated molecules, molecules with druglike and non-druglike properties. Kathleen Petri Seiler, Gregory A. George, Mary Pat Happ, Nicole E. Bodycombe, Hyman A. Carrinski, Stephanie Norton, Steve Brudz, John P. Sullivan, Jeremy Muhlich, Martin Serrano, Paul Ferraiolo, Nicola J. Tolliday, Stuart L. Schreiber, and Paul A. Clemons ChemBank: a small-molecule screening and cheminformatics resource database. Nucl. Acids Res. 2008 36: D351-D359 | Compound Database, Compound searching, prescription drugs |
| LINK | PubChem: An information resource linking chemistry and biology | Compound Database |
| LINK | Chemical thesaurus : database including chemical entities, interactions, reactions, processes | Compound Database |
| LINK | Chemical suppliers and collections | Compound Database |
| LINK | Top 200 prescriptions in 2002 (structure and name of the compounds) | Compounds drugs |
| LINK | prescription drugs (structure and name of the compounds). Molecule of the month | prescription drugs |
| LINK | Web directory about compound collections and many related links, database search | Compound Database, Compound searching |
| LINK | Free collections, about 10000 molecules, if you collaborate with the group | Compound Database |
| LINK | Free collections | Compound Database |
| LINK | Crystallography Open Database | Crystallography Open Database |
| LINK | NMRShiftDB - Free collection, some molecules are in 3D (Steinbeck 2001; Steinbeck et al. 2003; Steinbeck and Kuhn 2004) | Compound Database |
| LINK | Compound Database | |
| LINK | Utilities such as ligand clustering and ligand similarity search (Grotthuss et al. 2003) | Compound searching |
| LINK | ChemDB: Free collections and utilities such as similarity search | Compound Database, Compound searching |
| LINK | FAF-Drugs2: free ADME/tox filtering tool to assist drug discovery and chemical biology projects. Lagorce et al., BMC Bioinformatics. 2008 Sep 24;9:396 | ADMET-software |
| NO LINK | Modeling chemical mutagenicity. Langham JJ, Jain AN. J Chem Inf Model. 2008 48:1833-9. Contact the authors | ADMET-software |
| LINK | (see also: LINK). FAF-Drugs: Free collections (and ADME/tox) and utilities (Miteva et al. 2006) | 5 Compound collections in 3D (Single conf. and multiconf.) ADMET-online |
| LINK | ZINC: Free collections (Irwin and Shoichet 2005) (and links to commercial vendors) | Compound Databases (about 20), ADME/Tox, Compound searching |
| LINK | DUD is designed to help test docking algorithms by providing challenging decoys. It contains: * A total of 2,950 active compounds against a total of 40 targets * For each active, 36 "decoys" with similar physical properties (e.g. molecular weight, calculated LogP) but dissimilar topology. (J. Med. Chem., 49 (23), 6789 -6801, 2006. Benchmarking Sets for Molecular Docking. Niu Huang, Brian K. Shoichet and John J. Irwin) | Compounds for different targets, thrombin, FXa...and decoys |
| LINK | ChemMine: Free collections and similarity search utilities (Chen and Reynolds 2002; Girke et al. 2005) | Compound Database, Compound searching |
| LINK | Available Chemicals Directory (essentially commercial) | Compound Database, Compound searching |
| LINK | Commercial collection | Compound Database, Compound searching |
| LINK | Dictionary of small molecules. Kirill Degtyarenko, Paula de Matos, Marcus Ennis, Janna Hastings, Martin Zbinden, Alan McNaught, Rafael Alcantara, Michael Darsow, Mickael Guedj, and Michael Ashburner ChEBI: a database and ontology for chemical entities of biological interest. Nucl. Acids Res. 2008 36: D344-D350 | Compound Database |
| LINK | BindingDB: Measured binding affinities, macromolecule-ligand complexes (Chen et al. 2002c) | Compound Database, Macromolecules |
| LINK | Binding MOAD (Mother of All Databases) is a database of 9836 proteinÐligand crystal structures. All biologically relevant ligands are annotated, and experimental binding-affinity data is reported when available. Binding MOAD has almost doubled in size since it was originally introduced in 2004, demonstrating steady growth with each annual update. Several technologies, such as natural language processing, help drive this constant expansion. Along with increasing data, Binding MOAD has improved usability. The website now showcases a faster, more featured viewer to examine the proteinÐligand structures. Ligands have additional chemical data, allowing for cheminformatics mining. Mark L. Benson, Richard D. Smith, Nickolay A. Khazanov, Brandon Dimcheff, John Beaver, Peter Dresslar, Jason Nerothin, and Heather A. Carlson Nucleic Acids Research Advance Access published on November 30, 2007 | Compound Database, Macromolecules |
| LINK | The knowledge about interactions between proteins and small molecules is essential for the understanding of molecular and cellular functions. However, information on such interactions is widely dispersed across numerous databases and the literature. To facilitate access to this data, STITCH (Ôsearch tool for interactions of chemicalsÕ) integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drugÐtarget relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins. Each proposed interaction can be traced back to the original data sources. Our database contains interaction information for over 68 000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes and their interactions contained in the STRING database. Michael Kuhn, Christian von Mering, Monica Campillos, Lars Juhl Jensen, and Peer Bork STITCH: interaction networks of chemicals and proteins Nucleic Acids Research Advance Access published on December 15, 2007 | Compound Database, Macromolecules, genomes, 2200 drugs, 68000 chemicals |
| LINK | GLIDA: GPCRÑligand database for chemical genomics drug discoveryÑdatabase and tools update. Yasushi Okuno, Akiko Tamon, Hiroaki Yabuuchi, Satoshi Niijima, Yohsuke Minowa, Koichiro Tonomura, Ryo Kunimoto, and Chunlai Feng. Nucleic Acids Research Advance Access published on November 5, 2007 | GPCR-ligand Database |
| LINK | The molecular basis of drug action is often not well understood. This is partly because the very abundant and diverse information generated in the past decades on drugs is hidden in millions of medical articles or textbooks. Therefore, we developed a one-stop data warehouse, SuperTarget that integrates drug-related information about medical indication areas, adverse drug effects, drug metabolization, pathways and Gene Ontology terms of the target proteins. An easy-to-use query interface enables the user to pose complex queries, for example to find drugs that target a certain pathway, interacting drugs that are metabolized by the same cytochrome P450 or drugs that target the same protein but are metabolized by different enzymes. Furthermore, we provide tools for 2D drug screening and sequence comparison of the targets. The database contains more than 2500 target proteins, which are annotated with about 7300 relations to 1500 drugs; the vast majority of entries have pointers to the respective literature source. A subset of these drugs has been annotated with additional binding information and indirect interactions and is available as a separate resource called Matador. SuperTarget and Matador are available at http://insilico.charite.de/supertarget and http://matador.embl.de. Stefan Gunther, Michael Kuhn, Mathias Dunkel, Monica Campillos, Christian Senger, Evangelia Petsalaki, Jessica Ahmed, Eduardo Garcia Urdiales, Andreas Gewiess, Lars Juhl Jensen, Reinhard Schneider, Roman Skoblo, Robert B. Russell, Philip E. Bourne, Peer Bork, and Robert Preissner. SuperTarget and Matador: resources for exploring drug-target relationships. NAR 2007 or 2008 | Compound Database, Macromolecules |
| LINK | PDBbind: macromolecules with co-crystallized ligands and experimental binding affinities (Wang et al. 2005) | Compound Database, Macromolecules |
| LINK | Scorpio (structure-calorimetry of reported protein interactions online): This is a FREE online repository of protein-ligand complexes which have been structurally resolved and thermodynamically characterised | Compound Database with experimental values |
| LINK | KiBank: Proteins with co-crystallized ligands and experimental binding affinities (Zhang et al. 2004) | Compound Database, Macromolecules |
| LINK | RELIBASE: Proteins with co-crystallized ligands (Hendlich 1998; Bergner et al. 2001; Hendlich et al. 2003) | Compound Database, Macromolecules |
| LINK | CCDC/Astex validation test set: 305 protein-ligand complexes to calibrate docking and scoring tools (Nissink et al. 2002). There is now a shorter list with 85 complexes that have been investigated interactively. See Harthorn et al. J Med Chem 2007, in press. Diverse, high quality test set for the validation of protein-ligand docking performance | Compound Database, Macromolecules |
| LINK | SuperDrug database: contains 2.396 compounds | Drug Database |
| LINK | Similarity ensemble approach (SEA). The Similarity ensemble approach relates proteins based on the set-wise chemical similarity among their ligands. It can be used to rapidly search large compound databases and to build cross-target similarity maps | Drug Database |
| LINK | The SuperSite is an encyclopedia that is dedicated to a ligand and binding site oriented view of the protein structural space. SuperSite integrates evolutionary information in the proteins as well as predicted binding sites from LigsiteCSC. A point set match algorithm is implemented that allows to screen the surface of a protein for the occurrence of possible binding sites as well as a similarity screen for similar compounds based on fingerprints | Drug Database |
| LINK | LPDB database: ligand-protein. Brooks et al. Univ Michigan | Drug-Ligand Database |
| LINK | DrugBank: Numerous data about drugs and targets including drugs already in use (Wishart et al. 2006) | Drug Database |
| LINK | AffinDB: Proteins with co-crystallized ligands and experimental binding affinities (Block et al. 2006) | Compound Database, Macromolecules. Link does not work Feb 2007... |
| LINK | SMILIB: tool to create virtual libraries | Virtual Database generator in smiles |
| LINK | SChiSM2: Create Interactive Web Page Annotations of Molecular Structures Using Jmol | Annotate compounds |
| LINK | sMOL Explorer is a 2D ligand-based computational tool that provides three major functionalities: data management, information retrieval and extraction, and statistical analysis and data mining through Web interface. With sMOL Explorer, users can create his/her own database by adding each small molecule via a drawing interface or uploading the data files from internal and external projects into the sMOL database. Then, the database can be browsed and queried with textual and structural similarity search. The molecule can also be submitted to search against external public databases including PubChem, KEGG, DrugBank and eMolecules. Moreover, users can easily access a variety of data mining tools to perform analysis including (1) finding the frequent substructure, (2) clustering the molecular fingerprints, (3) identifying and removing irrelevant attributes from the data, and (4) building the classification model of biological a ctivity. sMOL Explorer has been developed as a collection of Java Server Pages (JSP) and Servlets running on the Apache Tomcat web server, utilizing MySQL database management and several chemical informatics libraries such as CDK, JOELib, and Open Babel for data manipulation, and connecting to various data analysis and mining methods from the Weka library and R statistical environment. After the installation, only a web browser is needed for using sMOL Explorer. Supawadee Ingsriswang; Eakasit Pacharawongsakda (2007), "sMOL Explorer: an open source, web-enabled database and exploration tool for Small MOLecules datasets", Bioinformatics | Data managment - Web interface small molecules |
| LINK | Ligand-Based methods | Ligand-based screening |
| LINK | Ilib Diverse: tool to create virtual drug-like libraries | Virtual Database generator |
| LINK | The US National Cancer Institute collections including natural products | Compound Database |
| LINK | Drug3k: Prescription drug information for consumers | Prescription drug information for consumers |
| LINK | ||
| LINK | Compilation of web sites that offer chemistry databases/search services, data about toxic molecules, hazardous substances, database browser | Compound Database, ADME/Tox |
| LINK | A free database of commercially available solvents searchable by many properties | Solvent Database |
| LINK | Course chemoinformatics | Chemo courses |
| LINK | Software for Atomic Scale Education & Research | software for education |
| LINK | Educational Sources from the Internet | online courses |
| LINK | Models of main functional groups, courses in organic chemistry | Chemistry courses |
| LINK | Chemistry courses | |
| LINK | MoSS - Molecular Substructure Miner. A program to find frequent molecular substructures and discriminative fragments in a database of molecule descriptions | Compound searching |
| LINK | MoFa: Molecular fragment miner | Compound searching |
| LINK | Main chemical-structures | Compound Database |
| LINK | View properties, purchase compounds | Compound Database |
| LINK | View structures and data of Open NCI DB compounds | Compound Database |
| LINK | Find compound properties | Compound searching |
| LINK | Similarity search and other tools | Compound searching |
| LINK | Chemspider | Compound searching |
| LINK | Chemistry Databases on the Web | Chemistry Databases |
| LINK | The web of chemical informatics | The web of chemical informatics |
| LINK | With eMolecules you can draw your chemical structure and instantly search millions of molecules from across the Web and from chemical suppliers worldwide | Compound searching |
| LINK | SuperLigands (Michalsky et al. 2005): a database of ligand structures derived from the Protein Data Bank with similarity searches and other tools | Compound Database from the PDB, Compound searching |
| LINK | Chemistry and biology database: numerous links (databases, tools) valuable for drug design projects | Compound Database, macromolecules links to programs |
| LINK | Small molecules from the PDB | Compound Database from the PDB |
| LINK | ChemID Plus: chemical name, physical and toxicological properties | Compound Database, ADME/Tox |
| LINK | The directory of chemistry on the WWW since 1993 | Numerous chemistry links |
| LINK | Compound collection and building blocks | Compound Database |
| LINK | QueryChem (Klekota et al. 2006): searches public databases using text and structure | Compound Database, Compound searching |
| LINK | The Prestwick Chemical Library is a unique collection of 1120 high-purity chemical compounds (all off patent) carefully selected | Off patent compound collections for experimental testing |
| LINK | The Spectrum Collection 2000 biologically active and structurally diverse compounds from our libraries of known drugs, experimental bioactives, and pure natural products. Refs: J Virology 77: 10288 (2003); Ann Rev Med 56: 321 (2005). SDF file available | Structurally diverse compounds for experimental screening and in silico work |
| LINK | SeqChem is an internet based company, specialising in biochemicals and other natural products. They provide a simple and cost effective way to fullfil chemical needs | Compounds for experimental screening |
| LINK | DTP maintains a repository of synthetic and natural products that have been evaluated as potential anticancer and anti-HIV agents. This repository has an historic inventory of more than 140,000 non-discreet compounds that have been submitted to DTP from a variety of sources worldwide. These materials, not based on a proprietary framework, represent unique structural diversity. The collection contains both synthetic compounds and fully characterized pure natural products. Chemical structures of these substances are those assigned by the originator of the material. Please note that in the vast majority of cases the compounds have not been analyzed for the accuracy of the structural information or for the purity of the sample. The DTP distributes samples from the open repository in two modes: As small numbers of specific agents: Procedure for requesting specific samples As pre-plated sets of compounds for screening: Procedure for requesting plated samples Plated Sets for Screening Diversity set - 1990 compounds for screening Mechanistic set - 879 compounds available Challenge set - 57 diverse compounds with unknown mechanisms of cell kill Natural Product set - 235 available compounds | Compound collections for experimental or in silico screening |
| LINK | Marvel Library - A Collection of Over 9000 Unique Compounds. History: The Marvel Storeroom was founded in 1961.Ê It began with the donation of the personal compound collection of Professor Carl Shipp Marvel to the UIUC Chemistry Department upon his retirement in 1961. It served as a free chemical repository for valuable, but no longer needed chemicals to be shared among all members of the Department. This resource was discontinued in 2006, as the questionable quality and identity of much of the library posed a safety risk. Prior to this event, the Hergenrother group went through the Storeroom and salvaged usable compounds with interesting structures. These compounds were added to the Marvel Library Compound Collection (MLCC), aÊ high-throughput screening (HTS) library in a 384-well format in DMSO maintained by the Hergenrother group. All compounds synthesized by the Hergenrother group are submitted to this respository for storage and screening purposes. The MLCC also contains compounds contributed from various research groups on campus. The compounds contained in the library are a testament to the diverse, rigorous research that has made the University of Illinois a world leader in the chemical sciences. | Compound collection for experimental or in silico screening |
| LINK | Human Metabolome Database: contains information about small molecule metabolites found in the human body | Human Metabolome Database |
| LINK | The Human Metabolome Library (HML) is a one-stop chemical resource to order/acquire one or more compounds to confirm, validate or quantify suspected metabolites in tissues or biofluids. | The Human Metabolome Library |
| LINK | Protein Ligand Database (v1.3). The PLD is a resource containing biomolecular data, including binding energies, Tanimoto ligand similarity scores and protein sequence similarities of protein-ligand complexes. The PLD(v1.3) currently has data on 485 protein ligand complexes. Dushyanthan Puvanendrampillai and John B. O. Mitchell. Bioinformatics 2003, 1856-57 | Protein Ligand Database |
| LINK | ScreeningAssistant and removal of duplicates. Tools to manage compound collections. ADME. AurlienÊMonge, AlbanÊArrault, ChristopheÊMarot and LucÊMorin-Allory. Molecular Diversity. Volume 10, Number 3 / August, 2006. 1381-1991 | Tools to manage compound collections. ADME |
Table V: 2D to 3D small molecules and 2D or 3D search and de novo ligand builder
| URLs | Short summary | Keywords |
| LINK | OSRA: Optical Structure Recognition, take the 2D drawing of a compound and get the SMILES | Images to SMILES |
| LINK | PASS similarity search | Similarity search |
| LINK | 2D to 3D based on CDK (Steinbeck et al. 2006) | Small molecules 2D-to-3D |
| LINK | 2D to 3D conversion and other tools | Small molecules 2D-to-3D |
| LINK | ||
| LINK | 2D to 3D conversion | Small molecules 2D-to-3D |
| LINK | Corina: 2D to 3D conversion | Small molecules 2D-to-3D |
| LINK | Omega: 2D to 3D conversion | Small molecules 2D-to-3D |
| LINK | ICM: 2D to 3D conversion | Small molecules 2D-to-3D |
| LINK | XDrawChem: Possible 2D to 3D conversion with BUILD3D | Small molecules 2D-to-3D |
| LINK | Smiles to 3D SDf and then structural optimization of the 3D structure mmff. Package in C with source code for Mac intel and Linux. Thanks to Kevin Gilbert who wrote the code. Rajarshi Guha updated command line parameter handling and the build scripts. | Small molecules 2D-to-3D - Free package with source code |
| LINK | Possible 2D to 3D (van Aalten et al. 1996; Schuttelkopf and van Aalten 2004) | Small molecules 2D-to-3D |
| LINK | 2D to 3D with Corina | Small molecules 2D-to-3D |
| LINK | EasyMol: A Java tool to design 2D molecules and render them in 3D | Small molecules 2D-to-3D |
| LINK | 3DFS is a program to search 3D databases for compounds matching a pharmacophore query (Wang and Zhou 1999) | Compound searching |
| LINK | SAAMCO (Similarity of Amino Acid Motifs to Compounds) is a robust and efficient workflow for a large-scale screening of small molecules databases against PDB structures. It relies on identifying small molecules with substituents that topologically and structurally resemble key amino acid side chains. Identification of Potential Small Molecule Peptidomimetics Similar to Motifs in Proteins, I. Baran, R.S. Varekova, L. Parthasarathi, S. Suchomel, F. Casey and D.C. Shields. Journal of Chemical Information and Modeling 47(2),pp464-474, 2008 | Compound searching, ligand-based, peptidomimetic |
| LINK | SLIMS is a laboratory information management system suitable for small labs. SLIMS is geared toward chemoinformatics and biological assays but can be extended with new datatypes. Brian Kelley | Chemical data storage - database |
| ftp2.ipc.pku.edu.cn | LigBuilder (Wang et al. 2000b): Based on the three-dimensional structure of the target protein, it can automatically build ligand molecules within the binding pocket | Compound searching, ligand-based |
| LINK | CONTACT THE AUTHORS OR GET THE APPLICATION IN THE SUPPL. We propose a systematic method to predict ligand-protein interactions, even for targets with no known 3D structure and few or no known ligands. Following the recent chemogenomics trend, we adopt a cross-target view and attempt to screen the chemical space against whole families of proteins simultaneously. The lack of known ligand for a given target can then be compensated by the availability of known ligands for similar targets. We test this strategy on three important classes of drug targets, namely enzymes, G-protein coupled receptors (GPCR) and ion channels, and report dramatic improvements in prediction accuracy over classical ligand-based virtual screening, in particular for targets with few or no known ligands. Availability: All data and algorithms are available as supplementary material. Protein-ligand interaction prediction: an improved chemogenomics approach. Bioinformatics Advance Access published August 1, 2008. Laurent Jacob and Jean-Philippe Vert Contact: Laurent.Jacob at ensmp.fr | structure-based, ligand-based, biostatistics |
| LINK | SurflexSim by Jain, VLS based on the ligand structure | Compound searching, ligand-based |
| LINK | PharmaGist: Predicting molecular interactions is a major goal in rational drug design. Pharmacophore, which is the spatial arrangement of features that is essential for a molecule to interact with a specific target receptor, is important for achieving this goal. PharmaGist is a freely available web server for pharmacophore detection. The employed method is ligand based. It does not require the structure of the target receptor. Instead, the input is a set of structures of drug-like molecules that are known to bind to the receptor. We compute candidate pharmacophores by multiple flexible alignments of the input ligands. The main innovation of this approach is that the flexibility of the input ligands is handled explicitly and in deterministic manner within the alignment process. The method is highly efficient, where a typical run with up to 32 drug-like molecules takes seconds to a few minutes on a stardard PC. Another important characteristic of the method is the capability of detecting pharmacophores shared by different subsets of input molecules. This capability is a key advantage when the ligands belong to different binding modes or when the input contains outliers. PharmaGist: a webserver for ligand-based pharmacophore detection. Schneidman-Duhovny D, Dror O, Inbar Y, Nussinov R, Wolfson HJ. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W223-8. | Compound searching, ligand-based, Pharmacophore |
| LINK | Molprint2D, ligand-based, fingerprint VLS. Bender A, Mussa HY, Glen RC, Reiling S. Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): evaluation of performance. J Chem Inf Comput Sci. 2004 Sep-Oct;44(5):1708-18. | Compound searching, ligand-based |
| LINK | Ultra fast shape comparison via CDK | Compound searching, ligand-based |
| LINK | NEWLEAD is a computer program for the automatic generation of candidate structures. The input for the program is a set of fragments in the three-dimensional orientation corresponding to a given pharmacophore model. The treatment consists in connecting the fragments with spacers assembled from small chemical entities (atoms, chains or ring moieties). The results are new structures containing the fragments in the orientation defined in the input. The program offers the opportunity of rapidly applying a pharmacophore model in drug-design by generating automatically a set of chemical structures conforming to the model. | Compound searching - newlead |
| LINK | AURAmol allows a user to take a candidate 2D or 3D molecular shape and use it to search for similarly shaped molecules in large databases | Compound searching |
| LINK | Graph Theoretical Similarity Approach To Compare Molecular Electrostatic Potentials. J. Chem. Inf. Model., 48 (1), 109 -118, 2008. Ray M. Marn, Nestor F. Aguirre, and Edgar E. Daza. Tree analysis and representation of isopotential surface | Similarity search |
| LINK | MEssEM: A MOLECULAR QUANTUM SIMILARITY MEASURES SYSTEM OF PROGRAMS. Authors: J. Mestres, M. Sola, E. Besalu, M. Duran and R. Carbo (Molecular Similarity: Methodological Development and Applications of Quantum Molecular Similarity Measures to Chemical Reactivity and analysis of Charge Density Distributions) | Similarity search |
| LINK | Similarity search. Rarey, M. and Dixon, J.S. Feature trees: A new molecular similarity measure based on tree matching Journal of Computer-Aided Molecular Design, 12: 471 490, 1998. | Similarity search |
| LINK | A graphical tool for structure-activity studies on Windows. SOMFA is a new technique for 3D QSAR designed by Peter Winn and Daniel Robinson. The method is very simple and avoids statistical selection procedures such as PLS. All tests so far show it to be as good as other QSAR methods, and better than many. The SOMFA code and executable may be downloaded. | Structure-activity, SOMFA (on Windows only) |
| LINK | E-DRAGON is the electronic remote version of the well known software DRAGON, which is an application for the calculation of molecular descriptors developed by the Milano Chemometrics and QSAR Research Group of Prof. R. Todeschini. These descriptors can be used to evaluate molecular structure-activity or structure-property relationships, as well as for similarity analysis and highthroughput screening of molecule databases. | Compute molecular properties |
| LINK | Shape Signatures Tool. Dr. Randy Zauhar (USIP, Phila, PA, http://www.usip.edu/chemistry/faculty/biography.asp?id=37) and collaborators have developed (patent pending) a novel computational tool known as ÒShape SignaturesÓ that is useful for many applications in drug discovery such as in silico screening that rapidly matches small drugÐlike molecules against each other or against receptor pockets based on similarity in shape and electrostatic properties. Please check here also: http://tonga.usip.edu/zauhar/. See a review by Peter J. Meek, ZhiWei Liu, LiFeng Tian, Ching Y. Wang, William J. Welsh and Randy J. Zauhar. Shape Signatures: speeding up computer aided drug discovery. Drug Discovery Today Volume 11, Numbers 19/20 October 2006 | New ligand-based screening approach to rapidly reduce the size of the input library |
| LINK | VeraChem: packages to help computer aided drug discovery like for instance Vconf, a powerful and flexible conform- ational search application which processes an SDfile of drug-like compounds with arbitrary initial 2D or 3D conformations and Vcharge, that calculates accurate, conformation- independent, "ab initio-like" partial atomic charges for an SDfile of drug-like compounds in about 0.1 second per compound | VeraChem2D-3D structure generator and small molecules analysis |
| LINK | Balloon 2d to 3d structure generator | small molecule 2d to 3d structure generator |
| LINK | VEGA ZZ is the evolution of the well known VEGA OpenGL package and includes several new features and enhancements making your research jobs very easy. VEGA was originally developed to create a bridge between most of the molecular software packages only, but in the years, enhancing its features, it's evolved to a complete molecular modelling suite. This software is FREE for non-profit academic uses | small molecule 2d to 3d structure generator and many others |
| LINK | FROG online tool for 1d/2d to 3d | small molecule 2d to 3d structure generator |
| LINK | VEGA ZZ is the evolution of the well known VEGA OpenGL package and includes several new features and enhancements making your research jobs very easy. VEGA was originally developed to create a bridge between most of the molecular software packages only, but in the years, enhancing its features, it's evolved to a complete molecular modelling suite. This software is FREE for non-profit academic uses | small molecule 2d to 3d structure generator and many others |
Table VIa: Receptor 3D structures, homology modeling, structure prediction, Interaction databases
| URLs | Short summary | Keywords |
| LINK | GANGSTA+ is a non-sequential structure-alignment tool. Publication: Aysam Guerler and Ernst-Walter Knapp. Novel folds and their nonsequential structural analogs. Protein Science 17, 2008 | Structural bioinformatics research |
| LINK | Biskit is a modular, object-oriented Python library for structural bioinformatics research. It facilitates the manipulation and analysis of macromolecular structures, protein complexes, and molecular dynamics trajectories. Biskit also offers a platform for the rapid integration of external programs and new algorithms into complex workflows. Calculations are thus often delegated to established programs like Xplor, Amber, Hex, Prosa, Fold-X, T-Coffee, Hmmer and Modeller; interfaces to further software can be added easily. Moreover, Biskit simplifies the parallelisation of calculations via PVM (Parallel Virtual Machine). Biskit has been jointly developed by Raik Grunberg and Johan Leckner (then at the Pasteur Institute in Paris) with important contributions from Michael Habeck (now Max-Planck-Institut fur Entwicklun gsbiologie, Tuebingen, Germany), Michael Nilges (Institut Pasteur), Wolfgang Rieping (Institut Pasteur) and others | Python library for structural bioinformatics research |
| LINK | RapperTK is a versatile toolkit for conformational sampling under restraints. It is a generalization of Rapper (Depristo, deBakker et.al.) developed by Swanand Gore at Prof Sir Tom Blundell's lab, Crystallography and Biocomputing Group, Department of Biochemistry, University of Cambridge | Conformational sampling - loop generation |
| LINK | Links to Macromolecular structures in 3D (Chandonia JM et al., NAR 2004) | Databases of Macromolecules in 3D |
| LINK | The Protein Data Bank (Deshpande et al. 2005) | 3D structure database |
| LINK | The Entrez Structure Database (Wang et al. 2002b) | Macromolecule database |
| LINK | PDBCat can be used to manipulate and process PDB files using commonly available tools such as Perl, awk, etc. | Tools to manipulate PDB files |
| LINK | Atlas of protein side-chain interactions within known protein structures and interactions with DNA | Macromolecule interaction database |
| LINK | BIND: The Biomolecular Interaction Network Database (Bader et al. 2003) | Macromolecule interaction database |
| LINK | DIP (Xenarios et al. 2002): Database of interacting proteins | Macromolecule interaction database |
| LINK | (Zanzoni et al. 2002) stores data on functional interactions between proteins | Macromolecule interaction database |
| LINK | Andreas Ruepp, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Goar Frishman, Corinna Montrone, Michael Stransky, Brigitte Waegele, Thorsten Schmidt, Octave Noubibou Doudieu, Volker Stmpflen, and H. Werner Mewes CORUM: the comprehensive resource of mammalian protein complexes Nucl. Acids Res. 2008 36: D646-D650 | Macromolecule interaction database |
| LINK | Balaji Raghavachari, Asba Tasneem, Teresa M. Przytycka, and Raja Jothi DOMINE: a database of protein domain interactions Nucl. Acids Res. 2008 36: D656-D661 | Macromolecule interaction database |
| LINK | Taku Nakahara, Ryo Hashimoto, Hiroaki Nakagawa, Kenji Monde, Nobuaki Miura, and Shin-Ichiro Nishimura Glycoconjugate Data Bank:StructuresÑan annotated glycan structure database and N-glycan primary structure verification service. Nucl. Acids Res. 2008 36: D368-D371 | Glycosylation |
| LINK | ProtCom (Kundrotas and Alexov 2006): a collection of protein-protein transient complexes | Macromolecule interaction database |
| LINK | Wuming Gong, Dihan Zhou, Yongliang Ren, Yejun Wang, Zhixiang Zuo, Yanping Shen, Feifei Xiao, Qi Zhu, Ailing Hong, Xiaochuan Zhou, Xiaolian Gao, and Tongbin Li PepCyber:P~PEP: a database of human proteinÐprotein interactions mediated by phosphoprotein-binding domains. Nucleic Acids Research Advance Access published on December 26, 2007 | Macromolecule interaction database |
| LINK | The Biological General Repository for Interaction Datasets (BioGRID) database. Bobby-Joe Breitkreutz, Chris Stark, Teresa Reguly, Lorrie Boucher, Ashton Breitkreutz, Michael Livstone, Rose Oughtred, Daniel H. Lackner, Jurg Bahler, Valerie Wood, Kara Dolinski, and Mike Tyers. The BioGRID Interaction Database: 2008 update Nucleic Acids Research Advance Access published on November 13, 2007 | Macromolecule interaction database |
| LINK | Many structural bioinformatics tools | Tools to analyze macromolecules |
| LINK | Many tools for structural bioinformatics, loop prediction, simulation, small molecules (Alland et al. 2005) | Structural bioinformatics online |
| LINK | The UCLA-DOE Structure Evaluation server is a tool designed to help in the refinement of crystallographic structures and models (Bowie et al. 1991) | Validate protein structure |
| LINK | ERRAT is a protein structure verification algorithm (Colovos and Yeates 1993) | Validate protein structure |
| LINK | SCWRL3.0 is the most recent version of the SCWRL program for prediction of protein side-chain conformations (Canutescu et al. 2003) | Predict protein side chain conformation |
| LINK | SCit is a web server providing services for protein side chain conformation analysis and side chain positioning (Gautier et al. 2004) | Predict protein side chain conformation |
| LINK | Bodil (Lehtonen et al. 2004): biomolecular modeling package | Molecular modeling |
| LINK | Modeller (Sali and Blundell 1993): software package for homology or comparative modeling of protein 3D structures | Homology modeling |
| LINK | Jackal: protein structure modeling package (Petrey et al. 2003) | Homology modeling, loop prediction related tools |
| LINK | ||
| LINK | Wurst (Torda et al. 2004): web server for protein structure prediction with a structural scoring function, sequence profiles and optimized substitutions matrices | Protein structure prediction |
| LINK | PSIPRED (McGuffin et al. 2000) web servers performing secondary structure prediction, transmembrane topology prediction or protein fold recognition | Protein structure prediction |
| LINK | PredictProtein (Rost et al. 2004): webserver for homology modeling and protein function prediction | Homology modeling related tools |
| LINK | Prospect-PSPP (Guo et al. 2004): automatic computational pipeline for protein structure prediction | Protein structure prediction |
| LINK | Robetta (Kim et al. 2004): web server for protein structure prediction and analysis | Protein structure prediction |
| LINK | SPACE (Sobolev et al. 2005): suite of tools for protein structure prediction and analysis based on complementarity and environment. Analysis of mutations, side chain modeling, docking via Ligin... | Protein structure prediction |
| LINK | Java Protein Dossier (Neshich et al. 2004): web-based visualization tool including large collections of physicochemical parameters describing proteins structure, stability, function and interaction with other macromolecules | Protein structure analysis |
| LINK | Consolv: Tool to analyze protein-water interaction (Raymer et al. 1997) | Protein structure analysis. COMMENTS: SEE ALSO FIRST FOR PROTEIN FLEXIBILITY PREDICTION |
| LINK | CAMPO, SCR_FIND, CHC_FIND (Paiardini et al. 2005): web tools to analyze evolutionary conserved residues, structurally conserved regions and conserved hydrophobic contacts | Protein structure analysis |
| LINK | ||
| LINK | ||
| LINK | Pred-TMBB (Bagos et al. 2004): web server for predicting the topology of beta-barrel outer membrane proteins | Protein structure prediction |
| LINK | ProteinDBS (Shyu et al. 2004): web server for detection of similar protein tertiary structures | Protein structure analysis, Structural similarity search |
| LINK | FATCAT (Ye and Godzik 2004): web server for flexible structure comparison and structure similarity searching | Protein structure analysis, Structural similarity search |
| LINK | PreBi (Tsuchiya et al. 2006): Server for predicting biological homo protein-protein interfaces in crystal protein structures | Protein structure analysis, Interface search |
| LINK | CaspR (Claude et al. 2004): web server for automated molecular replacement, method of choice for X-ray crystallography structure determination when structural homologues are available in PDB, using homology modeling | Protein structure determination |
| LINK | PREDITOR (Berjanskii et al. 2006): Program for predicting dihedral angles from chemical shifts and/or sequential homology | Protein structure determination |
| LINK | Protein Peeling (Gelly et al. 2006): Tool for splitting a 3D protein structure into protein units which are an intermediate level of protein structure description between protein domains and secondary structures | Protein structure analysis |
| LINK | OPAAS (Shih et al. 2006): web server for optimal, permuted and other alternative alignments of protein structures | Structural similarity search |
| LINK | Localizome (Lee et al. 2006): server for identifying transmembrane topologies and TM helices of eukaryotic proteins using domain information | Protein structure prediction |
| LINK | (Tyagi et al. 2006): platform for protein structure analysis using well defined library of short structural motifs (SSMs) known as structural alphabets | Protein structure prediction |
| LINK | SABBAC (Maupetit et al. 2006): online structural alphabet-based protein backbone reconstruction from alpha-carbon trace | Protein structure prediction |
| LINK | (Chen et al. 2006): automated homology modeling server using a consensus strategy between psi-blast, impala and T-coffee with a final 3D structure modeled with Modeller | Homology modeling, related tools |
| LINK | ArchPRED (Fernandez-Fuentes et al. 2006): template based loop structure prediction server | Loop structure prediction |
| LINK | TransFold (Waldispuhl et al. 2006): web server for predicting the structure and residue contacts of transmembrane beta-barrels | Protein structure prediction |
| LINK | Harmony (Pugalenthi et al. 2006): web server for the assessment of protein structures | Protein structure validation |
| LINK | RosettaDesign (Liu and Kuhlman 2006): Server for identifying low energy amino acid sequences from the backbone coordinates of the target structure | Protein structure prediction |
| LINK | CODA (Deane and Blundell 2001): combined algorithm for predicting loops | Loop structure prediction. COMMENTS: THE LINK DOES NOT WORK, THE SERVICE SHOULD STILL BE AVAILABLE IN THE FUTURE. PLEASE CONTACT AUTHORS |
| LINK | ProteMiner (Chang et al. 2004): software package that searches the PDB for proteins containing a substructure similar to the one specified by the user | Structural similarity search |
| LINK | MolProbity (Davis et al. 2004): web server for structure validation and all-atoms contact analysis for nucleic acids and their complexes | Protein structure validation |
| LINK | Decoys R (Samudrala and Levitt 2000): database of computer generated conformations of proteins sequences that possess some characteristics of native proteins | Protein structure validation |
| LINK | iSee (Abagyan et al. 2006): software package including the structural genomics workflow into one file, from DNA to protein structure, using the Molsoft ICM-browser technology | Protein structure analysis, annotation |
| LINK | Automatic threading, optimization modeling and evaluation, homology modeling (Douguet and Labesse 2001) | Protein structure prediction |
| LINK | Ian M. Overton, C. A. Johannes van Niekerk, Lester G. Carter, Alice Dawson, David M. A. Martin, Scott Cameron, Stephen A. McMahon, Malcolm F. White, William N. Hunter, James H. Naismith, and Geoffrey J. Barton TarO: a target optimisation system for structural biology. Nucl. Acids Res. 2008 36: W190-W196 | Protein structure prediction |
| LINK | Christian Cole, Jonathan D. Barber, and Geoffrey J. Barton. The Jpred 3 secondary structure prediction server. Nucl. Acids Res. 2008 36: W197-W201. A Secondary Structure Prediction Server | Protein structure prediction |
| LINK | PROTEUS2 is a web server designed to support comprehensive protein structure prediction and structure-based annotation. PROTEUS2 accepts either single sequences (for directed studies) or multiple sequences (for whole proteome annotation) and predicts the secondary and, if possible, tertiary structure of the query protein(s). Unlike most other tools or servers, PROTEUS2 bundles signal peptide identification, transmembrane helix prediction, transmembrane beta-strand prediction, secondary structure prediction (for soluble proteins) and homology modeling (i.e. 3D structure generation) into a single prediction pipeline. Using a combination of progressive multi-sequence alignment, structure-based mapping, hidden Markov models, multi-component neural nets and up-to-date databases of known secondary structure assignments, PROTEUS2 is able to achieve among the highest reported levels of predictive accuracy for signal peptides (Q2=94%), membrane spanning helices (Q2=87%) and secondary structure (Q3 score of 81.3% ). PROTEUS2's homology modeling services also provide high quality 3D models that compare favorably with those generated by SWISS-MODEL (within 0.2 RMSD). The average PROTEUS2 prediction takes ~2 minutes per query sequence. Source code is also freely available. Scott Montgomerie, Joseph A. Cruz, Savita Shrivastava, David Arndt, Mark Berjanskii, and David S. Wishart. PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation. Nucl. Acids Res. 2008 36: W202-W209 | Protein structure prediction |
| LINK | Numerous information and links: protein interaction network and databases of complexes can be found at the JCB Protein-Protein Interaction Website | Numerous links and tools for macromolecular interactions |
| LINK | PSIbase (Gong et al, Bioinformatics 2005): a database of Protein Structural Interactome map (PSIMAP) | Protein interaction database |
| LINK | Structural Interactome Map of all Proteins | PSIbase is a molecular interaction database |
| LINK | membrane protein database | |
| LINK | SCOPPI: a structural classification of protein-protein interfaces (Winter et al ) | Protein-protein database |
| LINK | The first release of the DOCKGROUND (Douguet et al. 2006) resource implements a comprehensive database of co-crystallized (bound-bound) protein-protein complexes, providing foundation for the upcoming expansion to unbound (experimental and simulated) protein-protein complexes, modeled protein-protein complexes and systematic sets of docking decoys | Database of experimental complexes |
| LINK | ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. This novel method makes it possible to accurately dock atomic structures into low-resolution electron-density maps in times ranging from seconds to a few minutes. The high efficiency achieved with simulated and experimental test cases preserves the exhaustiveness needed in these heterogeneous-resolution merging tools. Electron miscroscopy. Garzon JI, Kovacs J, Abagyan R, Chacon P. Bioinformatics. 2006 Dec 6; [Epub ahead of print] | Docking modules into low resolution electron-density maps |
Table VIb: Pocket prediction, functional sites, interfaces (see also VIa)
| URLs | Short summary | Keywords |
| LINK | Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram | Surface analysis |
| LINK | PHECOM, tools to find pockets - Kawabata and Go, Proteins, Detection of pockets on protein surfaces...2007, in press. Contact the authors | Pocket detection |
| LINK | Server to predict binding sites, Q-site and pocketfinder (Laurie and Jackson 2005) | Pocket detection |
| LINK | ||
| LINK | CASTp (Dundas et al. 2006): Server to predict binding site - Binding sites and active sites of proteins and DNAs are often associated with structural pockets and cavities | Binding site prediction for drug design |
| LINK | This is an integrated resource, which provides information about ligands, sequence and structure motifs, their relative position and the neighbour environment. The details are derived from the PDB together with a mapping to other motif and active-site sources. All data are stored in a relational database, accessible through this interactive service for fast search and visualization capabilities. Search criteria can combine sequence motifs, structure motifs, protein sequence, 3D properties (like phi/psi and chi angles, CA and side-chain positions), secondary structure elements, 3D associations of small motifs, protein side-chain and main-chain bonds and protein-ligand interactions. We also offer different views on the data and provide multiple sequence and multiple structure alignment tools. MSDmotif: exploring protein sites and motifs. BMC Bioinformatics. 2008 Jul 17;9:312. Golovin A, Henrick K | Binding site - Pocket - Sequence Ligand Structure |
| LINK | CAVER provides rapid, accurate and fully automated calculation of pathways leading from buried cavities to outside solvent in static and dynamic protein structures. Study of these pathways is important in drug design and molecular enzymology to understand binding of inhibitors to the receptors, substrate binding and product egress from the enzyme active sites. Calculated pathways can be visualized by graphic program PyMol dissecting anatomy and dynamics of entrance tunnels. CAVER: A New Tool to Explore Routes from Protein Clefts, Pockets and Cavities, BMC Bioinformatics 2006, 7: 316. Petrek M., Otyepka M., Banas P., Kosinova P., Koca J. and Damborsky J. | Binding site - Pocket |
| LINK | The global structures of apo and holo proteins Supporting Information for the work presented in: Brylinski M, Skolnick J. (2008) What is the relationship between the global structures of apo and holo proteins? Proteins 70, 363-77 | Binding site - prediction for drug design - Apo Holo - Flexibility Receptor |
| LINK | MolAxis is a tool for the identification of high clearance pathways or corridors which represent molecular channels in the complement space of proteins. It is extremely efficient because it samples the medial axis of the complement of the molecule, reducing the problem dimension to two, since the medial axis is composed of surface patches. It is designed to analyze proteins channels, calculate pore dimensions and analyze atom accessibility. MolAxis reads files in the standard Protein Data Bank format (PDB) containing a single frame or multiple frames generated by molecular dynamics (MD) simulations. MolAxis handles two distinct scenarios: It computes channels that connect a single point (like an inner chamber) to the bulk solvent, and it also computes transmembrane (TM) channels. MolAxis has a friendly web interface (see the Web Server tab). It also has a stand-alone version, statically compiled for linux, which can be downloaded. Eitan Yaffe, Dan Fishelovitch, Haim J. Wolfson, Ruth Nussinov, Dan Halperin. "MolAxis: Efficient and Accurate Identification of Channels in Macromolecules." PROTEINS: Structure, Function, and Bioinformatics. April 2008. | Binding site - prediction for drug design - Pocket - channels in macromolecules |
| LINK | PocketDepth: A new depth based algorithm for identification of ligand binding sites in proteins. J Struct Biol. 2007 Sep 15. Kalidas Y, Chandra N. | Binding site prediction for drug design |
| LINK | PROSURFER contains information about structural similarities with respect to the query surfaces. A pocket search algorithm detected 48347 potential ligand binding sites from the 9708 non-redundant protein entries in the PDB database. All-against-all structural comparison was performed for the predicted sites, and the similar sites with the Z-score ≥ 2.5 were selected. These results can be accessed by the PDB code or ligand name | Binding site prediction for drug design |
| LINK | AutoLigand code is included in the AutoDockTools release 1.4 and higher. See also http://www.scripps.edu/~rharris. To use, here are the advise of Rodney Harris: To run AutoLigand, first, make a 1 A grid box over the whole receptor (or the portion you are interested in). This is best done in a separate directory as docking runs are normally done with a 0.375 A grid. Choose to Set Map Types directly and choose C, OA, HD. To run AutoLigand from ADT, pull-down FILE/Browse Commands, then choose AutoDockTools, then AutoLigandCommand, click Load Selected Module and then dismiss the window. Next, pull-down the Compute menu and select AutoLigand/Run AutoLigand. To run AutoLigand from the command line, type: python [PATH]AutoLigand.py which will give you a usage statement. You need to run it from the directory where you have your map files. A new version of AutoLigand will be released in 2009 | Binding site prediction for drug design. Works with Pymol |
| LINK | PocketPicker, analysis of ligand binding-sites with shape descriptors. Martin Weisel, Ewgenij Proschak and Gisbert Schneider. Chemistry Central Journal 1-17, 2007, in press see also: http://gecco.org.chemie.uni-frankfurt.de/pocketpicker/index.html | Binding site prediction for drug design. Works with Pymol |
| LINK | Pymlp is a refurbished version of some former fortran code called MLPP. Calculate lipophilicity potential maps of protein for vmd and pymol | Binding site prediction for drug design |
| LINK | many tools to analyze protein surface, pockets...protein fingerprint | Binding site prediction for drug design |
| LINK | DMS is an open source program written in C for computing the molecular surface of a molecule. It can distribute the computation across multiple hosts for maximal performance. The surface computed is that defined by F. M. Richards (1977, Ann. Rev. Biophys. Bioeng.). In addition to the molecular surface, DMS can report the molecular surface area associated with each surface point, and surface normals at each surface point | Molecular_Surface |
| LINK | MSMS: M Sanner tool for surface and others | Molecular_surface |
| LINK | GETAREA 1.1: Solvent Accessible Surface Areas, Atomic Solvation Energies, and Their Gradients for Macromolecules. Fraczkiewicz, R; Braun, W. (1998) J. Comp. Chem., 19, 319 | Molecular_surface |
| LINK | ASA-View (or Asaview): Solvent Accessibility graphics for proteins | Molecular_surface |
| LINK | SCREEN: Server to predict binding site (Nayal and Honig 2006) | Binding site prediction |
| LINK | MEDock: Online tool to define binding site (Chang et al. 2005) | Binding site prediction |
| LINK | ConSurf (Glaser et al. 2003) identifies functional regions in proteins | Binding site prediction |
| LINK | Rate4Site (Pupko et al. 2002): an algorithmic tool for the identification of functional regions on proteins by surface mapping of evolutionary determinants within their homologues | Binding site prediction |
| LINK | PASS (Brady and Stouten 2000): Pocket detection method based upon the size, shape of buried volumes | Pocket detection |
| LINK | Voidoo (Kleywegt and Jones 1994): Pocket detection tool | Pocket detection |
| LINK | SurfNet (Laskowski 1995): Pocket detection tool | Pocket detection |
| LINK | Global and Restrained Docking Exploration Nexus 3D-GARDEN is a state-of-the-art comprehensive software suite and server for protein-protein docking with full high-performance computing functionality implementing multiple novel efficient methodologies: * TODE, using simplicial complex representation of the protein surfaces to generate and score an ensemble of complexed structures in the initial conformational state, which is naturally pre-enriched in structures with favourable shape complementarity * RABBIT, an efficient refinement method based on exhaustive search of torsion angles with tuned step sizes Please note that this program supersedes 3D-DOCK. | Macromolecular docking online |
| LINK | The FireDock server addresses the refinement problem of protein-protein docking solutions. The method simultaneously targets the problem of flexibility and scoring of solutions produced by fast rigid-body docking algorithms. Given a set of up to 1000 potential docking candidates, FireDock refines and scores them according to an energy function, spending about 3.5 seconds per candidate solution. To the best of our knowledge, this is the first webserver that allows performing large-scale flexible refinement and scoring of docking solutions online. N. Andrusier, R. Nussinov and H. J. Wolfson. FireDock: Fast Interaction Refinement in Molecular Docking. Proteins 2007, 69(1):139-59 | Macromolecular docking |
| LINK | Gramm: Tools for protein-protein docking. GrammX (Tovchigrechko and Vakser 2006): web interface of Gramm | Macromolecular docking |
| LINK | Macromolecular docking | |
| LINK | Intervor: Tools to analyze interfaces | Interface analysis |
| LINK | MolSurfer (Gabdoulline et al. 1999): a macromolecular interface navigator | Interface analysis |
| LINK | LIGIN: Molecular docking using surface complementarity. The LIGIN program (Sobolev et al. 1997) is also available as part of the WHATIF software package. | Macromolecular docking |
| LINK | Protein docking tools (PatchDock) and related (Shatsky et al. 2004; Schneidman-Duhovny et al. 2005). PatchDock, webserver for macromolecules and small molecules docking based on shape complementarity criteria | Macromolecular docking |
| LINK | PyDock: tool for protein-protein docking (Chelliah et al. 2006) | Macromolecular docking |
| LINK | Protein docking | Macromolecular docking |
| LINK | Crescendo (Chelliah et al. 2006): functional site prediction by the detection of protein-protein interaction sites | Binding site prediction. COMMENTS: the link does not work, please contact Juan http://mmb.pcb.ub.es/~juan/ and juan at mmb.pcb.ub.es |
| LINK | iMolTalk (Diemand and Scheib 2004): On-line tools including detection of the interface between two chains of a structure | Interface analysis |
| LINK | 3D-Dock (Gabb et al. 1997): software package for rigid-body protein-protein docking using shape complementarity, electrostatics, biochemical information , residue level pair potential score and a refinement tool | Macromolecular docking |
| LINK | Bipdock: Bielefeld Protein Docking Software | Macromolecular docking |
| LINK | ClusPro (Comeau et al. 2004): protein-protein docking webserver using 3 docking programs - DOT (Mandell et al. 2001), ZDOCK (Chen et al. 2003), GRAMM (Tovchigrechko and Vakser 2006) | Macromolecular docking |
| LINK | Protein Interactions Calculator (PIC) is a server which, given the coordinate set of 3D structure of a protein or an assembly, computes various interactions such as disulphide bonds, interactions between hydrophobic residues, ionic interactions, hydrogen bonds, aromaticÐaromatic interactions, aromaticÐsulphur interactions and cation-pi interactions within a protein or between proteins in a complex. K. G. Tina, R. Bhadra, and N. Srinivasan. Nucleic Acids Res. 2007 July; 35(Web Server issue): W473ÐW476. | Protein-protein energy computation |
| LINK | DOT (Mandell et al. 2001): protein-protein docking software with a surface grid applied to the fixed and the moved protein. Further refinement is performed via energy minimization and molecular dynamics | Macromolecular docking |
| LINK | ZDOCK (Chen et al. 2003): protein-protein docking software evaluating based on shape complementarity, desolvation energy and electrostatics. Best predictions from ZDOCK are given to RDOCK where they are minimized by CHARMM | Macromolecular docking |
| LINK | Protein-protein docking package (Daily et al. 2005) | Macromolecular docking |
| LINK | Steven J. Darnell, Laura LeGault, and Julie C. Mitchell KFC Server: interactive forecasting of protein interaction hot spots Nucl. Acids Res. 2008 36: W265-W269 | Hot-Spots |
| LINK | Emre Guney, Nurcan Tuncbag, Ozlem Keskin, and Attila Gursoy HotSprint: database of computational hot spots in protein interfaces Nucl. Acids Res. 2008 36: D662-D666 | Hot-Spots |
| LINK | Sergey Lyskov and Jeffrey J. Gray The RosettaDock server for local proteinÐprotein docking. Nucl. Acids Res. 2008 36: W233-W238; | Macromolecular docking |
| LINK | BDOCK: protein-protein docking software integrating the degree of burial of surface residues into protein-protein docking | Macromolecular docking |
| LINK | MolFit (Katchalski-Katzir et al. 1992): protein-protein docking software estimating the extent of geometric and chemical surface complementarity | Macromolecular docking |
| LINK | Hex (Ritchie and Kemp 2000): protein-protein docking and molecular superposition program | Macromolecular docking |
| LINK | ESCHER-NG (Ausiello et al. 1997): protein-protein and DNA-protein docking software | Macromolecular docking |
| LINK | FTDock (Fourier Transform Dock ) performs rigid-body docking on two biomolecules in order to predict their correct binding geometry(Katchalski-Katzir et al. 1992) | Macromolecular docking |
| LINK | GRID (Kastenholz et al. 2000): Tool for analysis of binding sites | Binding site prediction and analysis |
| LINK | SuperStar (Verdonk et al. 2001): Tool for analysis of binding sites | Binding site prediction and analysis |
| LINK | SitesBase (Gold and Jackson 2006b): Tool for analysis of binding sites (Gold and Jackson 2006a) | Binding site analysis |
| LINK | Prism (Ogmen et al. 2005) predicts and analyzes putative protein, protein interaction sites. | Binding site analysis, prediction |
| LINK | SiteEngines (Shulman-Peleg et al. 2005): recognition and comparison of binding sites and protein; protein interfaces | Binding site prediction, analysis |
| LINK | ||
| LINK | FastContact (Camacho and Zhang 2005): a free energy scoring tool for protein-protein complex structures | Macromolecular scoring |
| LINK | ProMate (Neuvirth et al., 2004): prediction of potential protein-protein binding sites | Binding site prediction |
| LINK | ODA (Optimal Docking Areas) (Fernandez-Recio et al. 2005) is a new method to predict protein-protein interaction sites on protein surfaces. It identifies optimal surface patches with the lowest docking desolvation energy values as calculated by atomic | Binding site prediction |
| LINK | SPIN-PP is a database of all protein-protein interfaces present in the PDB. A basic set of physico-chemical properties were then mapped on to these surfaces, which were then used to classify the interfaces into a surface property taxonomy. The mapped properties currently include surface curvature, electrostatic potential, based on formal charges, sequence variability, based on the HSSP alignments, and hydrophobicity, on an atom-based model | Macromolecule interaction database |
| LINK | SHARP² predicts the location of protein interaction sites on the surface of the 3D structure of a protein (Murakami, Jones, Bioinformatics 2006) | Predict binding site |
| LINK | InterPare: Most proteins function by interacting with other molecules. Their interaction interfaces are highly conserved throughout evolution to avoid undesirable interactions that lead to fatal disorders in cells. Rational drug discovery includes computational methods to identify the interaction sites of lead compounds to the target molecules. Identifying and classifying protein interaction interfaces on a large scale can help researchers discover drug targets more efficiently. (Gong et al., BMC Bioinfo 2005) | Interfaces |
| LINK | Analysis of interatomic Contacts in Ligand-Protein complexes Analysis of interatomic contacts in protein entries |
Analysis of interatomic Contacts |
| LINK | SCOWLP is a web-based relational database formed by eleven tables describing PDB interface interactions at atom, residue and domain level. A web application to handle and navigate through the interfacial data in an automatic and user-friendly fashion (Teyra et al, 2006) | Interfaces - databases |
| LINK | the ADP_EM method makes it possible to accurately dock atomic structures into low-resolution electron-density maps in times ranging from seconds to a few minutes Ref. Garzon JI, Kovacs, Abagyan, Chacon, Bioinformatics advance access published Dec 6, 2006 | Docking in electron-density maps derived from for instance electron microscopy |
| LINK | See also here http://mitchell-lab.org/FADE.php. The Fast Atomic Density Evaluator (FADE) and Pairwise Atomic Density Reverse Engineering (PADRE) programs are designed to aid in the molecular modeling of proteins. In particular, the programs can rapidly elucidate features of interest such as crevices, grooves and protrusions. The topographical information produced by FADE and PADRE can help researchers easily pinpoint the most prominent features of a protein, regions which are likely to participate in interactions with other molecules. In addition to providing shape descriptors to aid in analyzing single molecules, FADE can directly evaluate the level of shape complementarity for docked protein-protein complexes. [1] Mitchell, J.C., Kerr, R. and Ten Eyck, L.F., Rapid atomic density measures for molecular shape characterization, J. Mol. Graph. Model. 19(3): 324-329, 2001. [2] Kuhn, L.A., Siani, M.A., Pique, M.E., Fisher, C.L., Getzoff, E.D., and Tainer, J.A., The interdependence of protein surface topography and bound water molecules revealed by surface accessibility and fractal density measures, J. Mol. Biol. 228: 13-22, 1992. | Predict binding sites and analyze docked complexes |
| LINK | LIGSITEcsc is a web server for the automatic identification of pockets on protein surface using Connolly surface and degree of conservation. Bingding Huang and Michael Schroeder (2006), LIGSITEcsc: predicting protein binding sites using the Connolly surface and degree of conservation, BMC structural Biology, 6:19. | Predicting protein binding sites - Binding pockets |
| LINK | Dynapocket explore the dynamics of your pocket | Pocket analysis |
Table VII: comparing binding sites, protein function prediction (see also VIb)
| URLs | Short summary | Keywords |
| LINK | Annotated binding sites | Binding site analysis |
| LINK | PDBSiteScan automatically performs the best superposition of sites from PDBSite with the 3D structure of a protein under study | Binding site comparison |
| LINK | SiteBase (Gold and Jackson 2006b): compare nucleotide and ligand binding site | Binding site comparison |
| LINK | (Stark et al. 2003): detection of similarities between protein structures consisting of amino acids that are close in space | Structural similarity search |
| LINK | Multiple Alignment of Protein Binding Sites Recognizes Spatial Chemical Binding Patterns Common to a Set of Protein Structures. Protein binding sites which bind similar ligand and perfrom similar function share a certain 3D physico-chemical pattern. MultiBind aligns between a set of protein binding sites and recognizes the common spatial arrangement of physico-chemical properties ("receptor based pharmacophore"). MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W260-4. Shulman-Peleg A, Shatsky M, Nussinov R, Wolfson HJ. | Structural similarity search - receptor-based pharmacophore |
| LINK | Tools for analysis of binding sites and to find similar motifs based on a search in the PDB (Jambon et al. 2003) | Structural similarity search |
| LINK | SPASM (Kleywegt 1999): detection of similar motifs based on a search in the PDB | Structural similarity search |
| LINK | Catalytic site atlas (Porter et al. 2004): find similar catalytic sites | Structural similarity search |
| LINK | pvSoar (Binkowski et al. 2003): detection of a protein surface pattern derived from a pocket or a void against all known surface patterns from the CASTp database | Structural similarity search, Binding site comparison |
| LINK | LigASiteÑa database of biologically relevant binding sites in proteins with known apo-structures. Benoit H. Dessailly1, Marc F. Lensink, Christine A. Orengo and Shoshana J. Wodak. Nucleic Acids Research 2007 | Database of binding site |
| LINK | RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. Nucl. Acids Res. 2007 35: W578-W584. Michael Terribilini, Jeffry D. Sander, Jae-Hyung Lee, Peter Zaback, Robert L. Jernigan, Vasant Honavar, and Drena Dobbs | Analyzing and predicting RNA-binding sites |
| LINK | WoLF PSORT: Protein Subcellular Localization Prediction. Paul Horton, Keun-Joon Park, Takeshi Obayashi, Naoya Fujita, Hajime Harada, C.J. Adams-Collier, and Kenta Nakai. Nucl. Acids Res. 2007 35: W585-W587 | Protein Subcellular Localization Prediction |
| LINK | PAR-3D: a server to predict protein active site residues. Kshama Goyal, Debasisa Mohanty, and Shekhar C. Mande. Nucleic Acids Research 2007 | Predict protein active site |
| LINK | Sc-PDB: tool for analysis of binding sites (Kellenberger et al. 2006). On Dec 2008, the database contained 5278 protein-ligand complexes with 1766 unique proteins and 2393 unique ligands in corrected mol2 format. | Binding site analysis |
| LINK | Pdbfun (Ausiello et al. 2005): web server for the identification of local structural similarities between annotated residues in proteins | Structural similarity search |
| LINK | Ligand transposition server (Martin et al. 2006) | Binding site comparison |
| LINK | Docking with substructure query in a protein family | Binding site comparison |
| LINK | SiteEngine (Shulman-Peleg et al. 2005) recognizes regions on the surface of one protein that resemble a specific binding site of another | Structural similarity search, Binding site comparison |
| LINK | The ProFunc server (Laskowski et al. 2005) had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure | Binding site prediction |
| LINK | CPASS (Shulman-Peleg et al. 2005): website for active site comparison | Binding site comparison |
| LINK | eF-Site (Kinoshita et al. 2002): Electrostatic surface of functional sites | Electrostatic computations, binding site search |
| LINK | proSAT2 (Gabdoulline et al. 2006): Features for visualizing SwissProt and PROSITE functional annotations by mapping of information on variants and mutations from the UniProt KnowledgeBase and the BRENDA enzyme information system onto protein structures | Functional site visualization |
| LINK | FeatureMap3D (Wernersson et al. 2006): tool mapping protein features such as post-translational modifications, protease cleavage sites or exonic structure onto 3D structures of homologous proteins | Functional site visualization |
| LINK | ProKware (Hung et al. 2006): Integrated system containing interactive graphic interface and abundant protein property annotations a the structural level and domain-domain interaction in protein 3D structures | Functional site visualization |
| LINK | Protemot (Chang et al. 2006): server that carries out prediction of protein binding sites based on the structural templates automatically extracted from the PDB crystals | Binding site prediction. COMMENTS: link does not seem to work on Dec 2006 |
| LINK | Structural Analysis of Residue Interaction Graphs. This server converts a protein structure to a residue interactions graph (RIG) and calculates various network properties for each amino acid. | Interactions |
| LINK | Protein 3D Structure Comparison: MATRAS : MArkovian TRAnsition of Structure evolution. Many tools, search the PDB, align sequences...Kawabata T. "MATRAS: a program for protein 3D structure comparison" (2003). Nucleic Acids Res. Vol 31, 3367-9. Kawabata T., Nishikawa.K. "Protein tertiary structure comparison using the Markov transition model of evolution" (2000). Proteins, vol 41, 108-122 | Protein 3D Structure Comparison |
Table VIII: Target analysis, simulations, normal modes, MD...
| URLs | Short summary | Keywords |
| LINK | Lipid membrane in 3D: please check here also: http://persweb.wabash.edu/facstaff/fellers/ ; http://www.lrz-muenchen.de/~heller/membrane/membrane.html ; http://www.apmaths.uwo.ca/~mkarttu//downloads.shtml | Membrane - lipids in 3D |
| LINK | I-Mutant2.0, predicting stability changes upon mutation from the protein sequence or structure | Analysis of mutations |
| LINK | Prediction of side chain conformations and mutations on fixed backbone | Analysis of mutations |
| LINK | SRide (Magyar et al. 2005): server for identifying stabilizing residues in proteins | Analysis of mutations |
| LINK | MutDB services (Dantzer et al. 2005): interactive structural analysis of mutation data | Analysis of mutations |
| LINK | FoldX: empirical force field that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids (Guerois et al. 2002; Schymkowitz et al. 2005) | Analysis of mutations |
| LINK | Analysis of mutations | |
| LINK | predict protein aggregation | Analysis of mutations |
| LINK | Tinker online | Molecular modeling, simulations. Dec 2006, the link does not work, not sure what is going on ? |
| LINK | Towhee is a Monte Carlo molecular simulation code originally designed for the prediction of fluid phase equilibria using atom-based force fields and the Gibbs ensemble with particular attention paid to algorithms addressing molecule conformation sampling. The code has subsequently been extended to several ensembles, many different force fields, and solid (or at least porous) phases. | Molecular modeling, simulations, Monte Carlo |
| LINK | AMMP is a modern full-featured molecular mechanics, dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers | Molecular modeling, simulations |
| LINK | DL_POLY is a general purpose serial and parallel molecular dynamics simulation package developed at Daresbury Laboratory by W. Smith, T.R. Forester and I.T. Todorov | Molecular modeling, simulations |
| LINK | PINY_MD is capable of performing a wide variety of molecular dynamics, electronic structure, and geometry optimization calculations. Such capabilities include force-field based simulations on system ranging in complexity from simple molecular liquids and crystals to large biomolecular systems | Molecular modeling, simulations |
| LINK | Macromolecules and small molecules modeling | Molecular modeling, simulations |
| LINK | SIFT (Ng and Henikoff 2003): analyzes protein point mutations | Analysis of mutations |
| LINK | PolyPhen (Ramensky et al. 2002): analyzes protein point mutations | Analysis of mutations |
| LINK | WEBnm@: a web application for normal mode analysis of proteins (Hollup et al. 2005) to investigate for large amplitude movements. Normal modes are performed with MMTK (Hinsen 2000). | Molecular simulations |
| LINK | Sunhwan Jo, Miklos Vargyas, Judit Vasko-Szedlar, Benot Roux, and Wonpil Im. PBEQ-Solver for online visualization of electrostatic potential of biomolecules. Nucl. Acids Res. 2008 36: W270-W275; | Electrostatics |
| LINK | The PBEQ Solver calculates and visualizes the electrostatic potential of your molecule by solving the Poisson-Boltzmann (PB) equation. CHARMM online | Electrostatics |
| LINK | This PIPSA service is provided for the comparison of the electrostatic interaction properties of proteins. It permits the classification of proteins according to their interaction properties. PIPSA may assist in function assignment, the estimation of binding properties and enzyme kinetic parameters | Electrostatics |
| LINK | Online tools to compute protein electrostatics based on MEAD (Bashford and Karplus 1990): PCE (Protein Continuum Electrostatics) (Miteva et al. 2005) | Electrostatics |
| LINK | H++ (Gordon et al. 2005): a server for estimating pKas and adding missing hydrogens to macromolecules | Electrostatics |
| LINK | ProPka (Li et al. 2005): fast empirical method to predict pKas in proteins | Electrostatics |
| LINK | APBS (Baker et al. 2001): software package for the numerical solution of the Poisson-Boltzmann equation | Electrostatics |
| LINK | Open Protein Simulator (OOPS) is a program designed to serve as a test bed for different algorithms for protein folding, dynamics and structure prediction | Molecular simulations |
| LINK | Tools to analyze protein structures | Molecular modeling, structural analysis |
| LINK | Web resources for protein structure analysis, links to numerous web sites | Molecular modeling, structural analysis |
| LINK | WhatIf (Vriend 1990): versatile molecular modeling package | Molecular modeling, structural analysis |
| LINK | Dynamite is a free web-based service that predicts protein motions. It takes as input a pdb file. In return you get various movies and other representations of the protein's motions. | |
| LINK | elNemo is the Web-interface to The Elastic Network Model (Delarue and Sanejouand 2002), a fast and simple tool to compute the low frequency normal modes of a protein | Molecular simulations |
| LINK | GRASS (Nayal et al. 1999), Graphical Representation and Analysis of Structure Server | Molecular surface analysis |
| LINK | PROFbval (Schlessinger et al. 2006): method for predicting residue mobility based on amino-acid sequence. Identification of extremely rigid or flexible residues on the protein surface is helpful for identifying functionally important residues in proteins. A common measure of atom mobility in proteins is B-value data from x-ray crystallography structures. PROFbval is the first web server to predict normalized backbone B-values from amino-acid sequence | Protein flexibility prediction |
| LINK | Non covalent bond finder | Structural analysis |
| LINK | Structural analysis of proteins | Structural analysis |
| LINK | MutaProt (Eyal et al. 2001): Tool for structural analysis of point mutations: MutaProt | Analysis of mutations |
| LINK | Weka 3: Data Mining Software in Java | Data Mining Software |
| LINK | MODEL - Molecular Descriptor Lab for Computing structural and physichemical properties of molecules from their 3D structures | Molecular Descriptor from 3D |
| LINK | Open source clustering software | Clustering |
| LINK | Clustering software. SUBSET is a clustering program useful for the selection of a set of input vectors evenly scattered over the entire input space. Although SUBSET has been developed to cluster chemical databases, it does not contain any algorithm to handle molecular structures. Its input are the usual bitstrings, e.g, "1100011001...", which are widely used to represent presence and absence of molecular fragments and/or structural features. The only distance metric available yet is the Tanimoto coefficient. SUBSET has been applied to an evaluation of the diversity of chemical databases (see Johannes H. Voigt, Bruno Bienfait, Shaomeng Wang, and Marc C. Nicklaus, "Comparison of the NCI Open Database with Seven Large Chemical Structural Databases", J. Chem. Inf. Comput. Sci., 2001; 41(3): 702-712 | Clustering |
| LINK | SVMProt (Cai et al. 2003): protein functional family prediction | Structural analysis |
| LINK | This program places the required number of sodium ions around a system of electric charges, e.g., the atoms of a biological macromolecule (protein, DNA, protein/DNA complex) | Tools to prepare molecules for simulations |
| LINK | GULP is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids)(Gale 1997) | Molecular simulations |
| LINK | The Biomolecule Toolkit is a library for modeling biological macromolecules such as proteins, DNA and RNA. It provides a C++ interface for common tasks in structural biology to facilitate the development of molecular modeling, design and analysis tools | Molecular modeling |
| LINK | Monster (Salerno et al. 2004): web application for inferring potentially stabilizing non-bonding interactions in macromolecular structures | Structural analysis, mutations |
| LINK | DisEMBL (Linding et al. 2003): computational tool for prediction of disordered/unstructured regions within a protein sequence. | Structural analysis, mutations |
| LINK | Disopred2 (Ward et al. 2004): Prediction and functional analysis of native disorder in proteins | Structural analysis, mutations |
| LINK | AVP (Another Void Program) is a new method for the analysis of voids in proteins and packing quality in a single united program | Cavity search |
| LINK | YUP: A Molecular Simulation Program for Coarse-Grained and Multiscaled Models (Python) | Molecular simulations |
| LINK | oGNM (Yang et al. 2006): calculating the equilibrium dynamics of any structure submitted in PDB format, using the Gaussian network Model (GNM) | Molecular simulations, flexibility |
| LINK | ProtoMol: object-oriented component based framework for molecular dynamics simulations | Molecular simulations |
| LINK | PDB_Hydro (Azuara et al. 2006): Tools for mutating and solvating protein structures | Tools to prepare molecules for simulations |
| LINK | PHEPS (Kantardjiev and Atanasov 2006): fast pH-dependent electrostatic calculations for proteins | Electrostatics |
| LINK | PPD (Toseland et al. 2006): an integrated, web-accessible database of experimentally determined protein pKa values | Electrostatics |
| LINK | pKD (Tynan-Connolly and Nielsen 2006) : re-designing protein pKa values for a set of point mutations | Electrostatics, mutations |
| LINK | NOMAD-Ref (Lindahl et al. 2006): Tools using normal modes for structural refinement of large proteins | Molecular simulations |
| LINK | UMMS (Jang et al. 2006): Tool using normal mode to analyze the harmonic behaviors (fluctuations) of a macromolecule around its equilibrium and elastic network interpolation to generate the anharmonic pathways for conformational transitions of two metastable conformations of the same macromolecule | Molecular simulations, flexibility |
| LINK | Readout (Ahmad et al. 2006): structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition | Analysis of protein-DNA complex and DNA structure |
| LINK | CUPSAT (Parthiban et al. 2006): server for prediction of protein stability upon point mutations by assessment of the difference in free energy of unfolding between wild-type and mutant proteins using structural environment specific atom potentials and torsion angle potential | Analysis of mutations |
| LINK | FSolv: fast method for the determination of fractional contributions to solvation in proteins | Solvation |
| LINK | PMut (Ferrer-Costa et al. 2005): predicts the pathologic character of a punctual mutation in a protein | Analysis of mutations |
| LINK | Qgrid (Ahmad and Sarai 2004): webserver for detection of charged and hydrophobic clusters in proteins | Structural analysis, COMMENT: you may need to try several times the link |
| LINK | ILM (Ruan et al. 2004): web server combining two algorithms, iterated loop matching and maximum weighted matching, for predicting RNA secondary structures | RNA structure prediction |
| LINK | RDfolder (Ying et al. 2004): webserver for prediction of RNA secondary structure from two methods, random stacking of helical regions and helical regions distribution | RNA structure prediction |
| LINK | NAMD (Phillips et al. 2005): molecular dynamics package for simulation of large biomolecular systems | Molecular simulations |
| LINK | CURVES: software package for calculating a helical parameter description for any irregular nucleic acid segment with respect to an optimal, global helical axis | Nucleic acid analysis |
| LINK | MANIP (Massire and Westhof 1998): interactive tool for modeling of RNA structure | Nucleic acid analysis |
| LINK | FANTOM (Fast Newton-Raphson Torsion Angle Minimizer) calculates low-energy conformations of polypeptides and proteins, compatible with distance and dihedral angle constraints obtained typically from NMR experiments. Protein-solvent interaction is included with a fast routine GETAREA for the calculation of accessible surface areas of individual atoms and their gradients. FANTOM is suited for the exploration of low energy conformations of cyclic peptides and of flexible loops in proteins as well. In addition to the above uses, with the newly added program EXDIS, FANTOM is an efficient tool for homology modeling of proteins (von Freyberg et al. 1993; Soman et al. 2000) | Molecular simulations |
| LINK | CHARMM (Chemistry at HARvard Molecular Mechanics) is a program for macromolecular simulations | Molecular simulations |
| LINK | many perl scripts to analyze a protein, add ions, compute volume, add ions in a box of water, tools for Python, compute energy.. | Analyze protein structures |
| LINK | Scripts for manipulating molecules | scripts to help prepare organic molecules for simulation |
| LINK | Assisted Model Building with Energy Refinement. Amber refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos. The current version of the code is Amber version 10, which is distributed by UCSF | Analyze protein structures |
| LINK | Many modeling tools for proteins, parsing PDB files..and so on CHARMM, Amber...MMTSB tools, like rmsd, rms fit...center of gravity, radius of gyration...(Perl and C) | Analyze protein structures |
| LINK | Python macromolecular library..many tools to study PDB files, geometry, viewer... mmLib, Class for least-squares structural superposition... | Analyze protein structures |
| LINK | Many tools for proteins, statistics about your PDB file, volume... Uppsala Software Factory - Welcome ! Executables only but for different systems, Iris, Linux, and Mac OS X | Analyze protein structures |
| LINK | Roberto Mosca and Thomas R. Schneider RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes Nucl. Acids Res. 2008 36: W42-W46 | Analyze protein structures - RMSD |
| LINK | Raphael A. Bauer, Philip E. Bourne, Arno Formella, Cornelius Frmmel, Christoph Gille, Andrean Goede, Aysam Guerler, Andreas Hoppe, Ernst-Walter Knapp, Thorsten Pschel, Burghardt Wittig, Valentin Ziegler, and Robert Preissner. Superimpos: a 3D structural superposition server. Nucl. Acids Res. 2008 36: W47-W54; | Analyze protein structures - RMSD |
| LINK | B is a Java-based, on-line biomolecular modeling package | Molecular modeling |
| LINK | GROMACS (Van Der Spoel et al. 2005) is a package for performing standard MD simulations, energy minimizations, NMR refinement | Molecular simulations |
| LINK | Molecular Dynamics Extended Library (Database of Molecular Dynamics Trajectories) | Molecular simulation database |
| LINK | The Uppsala Electron Density Server (Kleywegt et al. 2004) | Protein X-ray structural analysis |
| LINK | BioShell is a suite of programs designed for pre- and post-processing in protein structure modeling protocols | Tools to prepare molecules for simulations |
| LINK | SNPeffect (Reumers et al., 2006): check potential impact of mutations | Analysis of mutations |
| LINK | SNPs3D (Yue et al, 2006): is a website which assigns molecular functional effects of non-synonymous SNPs based on structure and sequence analysis | Analysis of mutations |
| LINK | PicSNP (Chang et al 2001): is a catalog of non-synonymous SNP (Single Nucleotide Polymorphism) in the human genome | Analysis of mutations |
| LINK | topoSNP database (Stitziel, 2003): this site allows for the visualization of disease and non-disease associated non-synonymous single nucleotide polymorphisms and displays geometric and relative entropy calculations | Analysis of mutations |
| LINK | Protein Dipole Moments Server: Electrostatic properties can play a significant role in affecting the properties and activities of proteins, for example influencing how and where various substrates, inhibitors and other proteins bind. If these themselves have a large net charge or dipole, this effect might be particularly significant. While the precise electrostatic potential about a protein involves a detailed and complex calculation, one can often get a first clue by examining two very simple properties, the net charge and the dipole moment | Electrostatics: dipole moment |
| LINK | PAT {Gracy and Chiche, 2005, NAR web server}: a protein analysis toolkit for integrated biocomputing on the web | Structural Analysis |
| LINK | Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces...Shula Shazman, Gershon Celniker, Omer Haber, Fabian Glaser, and Yael Mandel-Gutfreund Nucleic Acids Research 2007 | Mutation and docking/binding |
| LINK | ProMateus: an open research approach to protein-binding sites analysis. Hani Neuvirth, Uri Heinemann, David Birnbaum, Naftali Tishby, and Gideon Schreiber Nucleic Acids Research 2007 | Mutation and docking/binding |
| LINK | 3D-partner: a web server to infer interacting partners and binding models. Yung-Chiang Chen, Yu-Shu Lo, Wen-Chang Hsu, and Jinn-Moon Yang. Nucleic Acids Research 2007. 2007 35: W561-W567 | Protein-protein binding site prediction - hotspots |
| LINK | siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins. Nucleic Acids Research 2007. W489-494. C. Axel Innis | Protein-protein binding site prediction - hotspots |
| LINK | firestarÑprediction of functionally important residues using structural templates and alignment reliability. Gonzalo Lpez, Alfonso Valencia, and Michael L. Tress. Nucleic Acids Research 2007. 2007 35: W573-W577 | Protein-protein binding site prediction - hotspots |
| LINK | FastContact: a free energy scoring tool for proteinÐprotein complex structures. P. Christoph Champ and Carlos J. Camacho Nucleic Acids Research 2007. 2007 35: W556-W560 | Protein-protein docking |
| LINK | MODPROPEP: a program for knowledge-based modeling of proteinÐpeptide complexes. Narendra Kumar and Debasisa Mohanty. Nucleic Acids Research 2007 | Peptide docking |
| LINK | HyPare is a newly designed tool based on the PARE algorithm (Predicting Association Rate Enhancement). With HyPare you can find hotspots for association, and thus, engineer molecules... | Mutation and docking/binding |
| LINK | Analysis of correlated mutations | Analysis of mutations and folding |
| LINK | OCA, a browser-database for protein structure/function | Structural Analysis |
| LINK | FoldIndex (Prilusky et al., 2005) tries to answer to the question: Will this protein fold? It's a dynamic and interactive process that estimates the local and general probability for the provided sequence, under specified conditions, to fold. | Structural Analysis, folding |
| LINK | The program PARE calculates the change in rate of association (kon) of mutant protein-protein interaction complexes from the change in the Debye Huckel energy of interaction | Structural Analysis, binding, mutations |
| LINK | The MORPH server (Krebs and Gerstein 2000) produces 2D and 3D animations of a plausible or semi-plausible pathway between two submitted protein subunit conformations. See also database of macromolecular movements. Receptor flexibility | Structural analysis |
| LINK | The RECON server (Kundrotas and Alexov 2006d) predicts residue contacts using correlated mutation method with set of filters to reduce the false positives | Analysis of the quality of the 3D structure |
| LINK | The PROFcon server (Punta and Rost 2005) uses neural network method that utilizes sequence information, secondary structure and solvent accessibility predictions, and the overall properties of the entire protein to predict residue contacts | Analysis of the quality of the 3D structure |
| LINK | The CORNET server (Fariselli et al. 2001) is a neural network based predictor that uses as input correlated mutations, sequence conservation, predicted secondary structure and evolutionary information | Analysis of the quality of the 3D structure |
| LINK | Atlas of Side-Chain and Main-Chain Hydrogen Bonding by Ian McDonald and Janet M Thornton | Structural analysis, Protein Structure, course |
| LINK | The SCHEMA energy function, RASPP, uses structural information to predict which fragments of proteins can be swapped without disrupting the integrity of the three-dimensional structure (Voigt et al., 2002; Silberg et al., 2003, Endelman et al., 2004). | Mutation, protein stability |
| LINK | COREX/BEST server: a web browser-based program that calculates regional stability variations within protein structures. Vertrees, Barritt, Whitten, Hilser, Bioinformatics 21, 2005, 3318-19 | Protein regional stabilities |
| LINK | DFprot server provides deformability/flexibily analysis of your 3D structure. Please submit a structure file in the pdb format (only CA atoms of amino acids and P atoms of DNA/RNA nucleotides will be considered). Jose Ignacion Garzn, Julio A. Kovacs, Ruben Abagyan, and P. Chacn. Dfprot:A webtool for predicting local chain deformability (in Press 2007, Bioinformatics). | Macromolecule Flexibility |
| LINK | AD-ENM server provides a spectrum of analyses for the dynamics of an elastic network model (ENM) built from a given macromolecular structure. Zheng, W. & Doniach, S. A comparative study of motor-protein motions by using a simple elastic network model. Proc. Natl. Acad. Sci. 100, 13253-58 (2003) | Macromolecule Flexibility |
| LINK | MoViES (Molecular Vibrations Evaluation Server), facilitate the use of a program to study vibrational dynamics of proteins and nucleic acids. Nucleic Acids Research 2004 32(Web Server Issue):W679-W685. Z. W. Cao, Y. Xue, L. Y. Han, B. Xie, H. Zhou, C. J. Zheng, H. H. Lin and Y. Z. Chen | Macromolecule Flexibility |
| LINK | ModLoop is a web server for automated modeling of loops in protein structures. The input is the atomic coordinates of the protein structure in the Protein Data Bank format, and the specification of the starting and ending residues of one or more segments to be modeled, containing no more than 20 residues in total. Andras Fiser and Andrej Sali. Vol. 19 no. 18 2003, pages 2500 to 2501. Bioinformatics | Protein loop prediction |
Table IX: Docking and/or scoring engines for small molecule-macromolecule interactions
| URLs | Short summary | Keywords |
| LINK | DOVIS: an implementation for high-throughput virtual screening using AutoDock. Zhang et al., BMC Bioinformatics. 2008 Feb 27;9(1):126 | Small molecule docking |
| LINK | GriDock The virtual screening front-end for AutoDock 4 | Ligand_docking |
| LINK | AutoDock (Goodsell et al. 1996), small molecule docking | Small molecule docking |
| LINK | BDT (is an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock (Vaque et al. 2006) | Interface for Autodock docking |
| LINK | Dockres (reads the log file of docking runs performed by Autodock (version 3.0.5) and extracts the top scoring poses. The extraction can be subject to various filters (e.g., the residue nearest to the ligand...). The program also calculates distributions of various properties of the ligand set (e.g., molecular weight, number of hydrogen bond donors) and the distribution of docking sites as well as the distribution of docking free energies per target residue | AutoDock post-docking processing |
| LINK | Information theory-based scoring (Kulharia et al., J Chem Inf Model. The tool could become available at Dr Richard Jackson' site | Scoring |
| LINK | Information theory-based scoring (Kulharia et al., J Chem Inf Model. The tool could become available at Dr Richard Jackson' site | Scoring |
| LINK | eHits (Zsoldos et al. 2006): Small molecule docking | Small molecule docking |
| LINK | FRED (McGann et al. 2003): small molecule docking. See the online demos to try many OpenEye applications | Small molecule docking |
| LINK | DOCK (Kuntz et al. 1982; DesJarlais et al. 1988; Kuntz 1992): Small molecule docking | Small molecule docking |
| LINK | MS-DOCK: MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening. Rigid body docking to reduce the size of the compound collection prior to flexible docking. Multi-conf generator. Sauton, Lagorce, Villoutreix, Miteva. BMC Bioinformatics (2008) 9:184 | Small molecule docking |
| LINK | ViewDock to analyze Dock data and tools for post-processing DOCK results (Springer et al. 2005) | Small molecule docking post-docking processing |
| LINK | PubDock, docking pubchem ligands (few targets have been done) | Small molecule docking - structure_based_VLS |
| LINK | Surflex (Jain 2003): Small molecule docking | Small molecule docking - structure_based_VLS |
| NO LINK | ISE-dock: based on Autodock. Gorelik B, Goldblum A. Proteins: 2008 71:1373-86. Contact the authors | Small molecule docking - structure_based_VLS |
| LINK | AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening. Pencheva T et al., BMC Bioinformatics. 2008 Oct 16;9:438 | Small molecule pre-processing and post-docking processing, flexibility - induced-fit |
| LINK | Plants (Korb et al. 2006): Small molecule docking. There is also a tool to prepare small molecules called SPORES | Small molecule docking |
| LINK | Gupta, A. Gandhimathi, A. Sharma, P. and Jayaram, B. (2007) ParDOCK: An All Atom Energy Based Monte Carlo Docking Protocol for Protein-Ligand Complexes. Protein and Peptide Letters. Vol 14. pp. 632-646 | Small molecule docking |
| LINK | Binding Affinity Prediction of Protein-Ligand (BAPPL) server computes the binding free energy of a non-metallo protein-ligand complex using an all atom energy based empirical scoring function. Jain, T. and Jayaram, B. (2005) An all atom energy based computational protocol for predicting binding affinities of protein-ligand complexes. FEBS Letters, 579, 6659-6666. | Small molecule scoring |
| LINK | Binding Affinity Prediction of Protein-Ligand binding site with Zinc | Small molecule scoring |
| LINK | Drug Design tools | Drug Design tools |
| LINK | PSO@Autodock is a fast flexible molecular docking tool for virtual screening is based on Particle Swarm Optimization and has been implemented in AutoDock3. It employs varCPSO-ls (velocity adaptive and regenerative Constriction Particle Swarm Optimization with local search) algorithm to predict the protein-ligand interaction with full flexible treatment of ligands. Vigneshwaran Namasivayam, Robert Gunther Chem Biol & Drug Des 2007 (70), 475-484. | Small molecule docking |
| LINK | Receptor based molecular docking (GlamDock): Small molecule docking. GlamDock: Development and Validation of a New Docking Tool on Several Thousand Protein-Ligand Complexes. Simon Tietze and Joannis Apostolakis. J. Chem. Inf. Model. 47, 1657Ð1672. Please contact the authors | Small molecule docking |
| Try but ftp | PSI-DOCK (Pei et al. 2006): Small molecule docking. ftp://ftp2.ipc.pku.edu.cn/pub/software | Small molecule docking |
| LINK | PEARLS (Han et al. 2006): Program for Energetic Analysis of Receptor-Ligand System | Scoring |
| LINK | GFscore (Betzi et al. 2006): A General Non-Linear Consensus Scoring Function for High-Throughput Docking | Scoring |
| Try ftp | SCORE (Wang et al. 1998) is an empirical method developed for estimating the binding affinity of protein-ligand complex with known three-dimensional structure. ftp://ftp2.ipc.pku.edu.cn/ | Scoring |
| LINK | DrugScore (Sotriffer et al. 2002): evaluate ligand-receptor interaction energy | Scoring |
| LINK | FOLD-X can compute binding energy (Guerois et al. 2002) | Scoring |
| LINK | (Chen et al. 2002b): Computed ligand binding energy | Help for scoring functions |
| LINK | Scoring using molecular interaction fingerprints - package available upon request to Dr. D. Rognan - Please see J Chem Inf Model 2007, 47, 195-207 - or directely from the website section Download | Scoring via molecular interaction fingerprints |
| LINK | HINT is a software package that utilizes experimental solvent partitioning data as a basis for an empirical molecular interaction model. The program calculates empirical atom-based hydropathic parameters that, in a sense, encode all significant intermolecular and intramolecular non-covalent interactions implicated in drug binding or protein folding. NOT FREE | Scoring |
| LINK | DOCK Blaster - A free virtual screening facility | Docking tools online project |
| LINK | Tools to build molecular-docking activity prediction models by PLS regression with iterative training and pose-selection. Descriptors include (i) docking score(s), (ii) pharmacophore features, (iii) multi-feature descriptors learned by decision trees | Scoring |
| LINK | HBAT(Hydrogen Bond Analysis Tool) is a tool to automate the analysis of hydrogen bonds present in a PDB Structure file. Other related tools available from HBAT Project are PDIA(Post Docking Interaction Analysis) and HBNG(Hydrogen Bond Network Graph) | Post-docking analysis |
| LINK | Xscore (Wang et al. 2002a): tool to predict binding energy between ligand and receptor | Scoring |
| LINK | The goal of the http://www.cgal.org/opensource_frame.html CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms to users in industry and academia in the form of a C++ library | Help for docking |
| LINK | Distributed Chemical Computing Using ChemStar: An Open Source Java Remote Method Invocation Architecture Applied to Large Scale Molecular Data from PubChem. J Chem Inf Model. 2008 Apr;48(4):691-703. Karthikeyan M, Krishnan S, Pandey AK, Bender A, Tropsha A | Tools to speed-up computations |
| LINK | GEMSTONE (Grid Enabled Molecular Science Through Online Networked Environments) an integrated framework for accessing grid resources that supports scientific exploration, workflow capture and replay, and a dynamic services oriented architecture. This framework provides researchers in the molecular sciences with a tool to discover remote grid application services and compose them as appropriate to the chemical and physical nature of the problem at hand | Tools to speed-up computations |
| LINK | learn about computer clusters | Training about computer clusters |
| LINK | OpenMolGrid: tools to speed-up computations | Tools to speed-up computations |
| LINK | tarFisDock (Li et al. 2006) docks ligands into the proteins targets in PDTD (Potential Drug Target Database), and outputs the top 2%, 5% or 10% candidates ranked by the energy score, including their binding conformations and a table of the related target information | Small molecule docking |
| LINK | Mathias Dunkel, Stefan Gunther, Jessica Ahmed, Burghardt Wittig, and Robert Preissner. SuperPred: drug classification and target prediction. Nucl. Acids Res. 2008 36: W55-W59; | Drug target classification |
| LINK | Kindock and Simdock (Martin et al. 2006) Tool for comparative docking of protein kinase ligands and ligand transposition server | Small molecule positioning |
| LINK | Small molecule positioning | |
| LINK | A molecular modeling, graphics, and drug design program. Performs fast shape docking like FRED and has tools similar to AutoDock. Problems so far, it runs only on Windows | Molecular docking |
| LINK | The Ligand Explorer (a.k.a LigPro) was designed for rapid inspections of protein-ligand interactions, such as hydrophilic interactions, hydrophobic interactions and the interactions with ordered H2O molecules. The development used MBT toolkit. This Ligand Explorer has been integrated into the reengineered RCSB Protein Data Bank(PDB). It can also be run as a standalone application on desktop to access local structure files and files on PDB's servers; we provide a one-click download from this web site. The program takes a standard Protein Data Bank file or a mmCIF structure file as input, dynamically generates the ligand list associated with the structure, automatically centers the view at the user-selected ligand and provides one-click inspections of different types of interactions. It can also be used to produce high quality images for publications. | Java Tools for interactive post-processing of docking studies |
| LINK | Many computer tools for small (or large) molecules. ARMS: Spatial Alignment with the RMS (Root Mean Square) method. ASV: Analytical calculation of van der Waals surfaces and volumes. CSR: The Combined SDM/RMS Algorithm for spatial alignment of two molecules. DOG: Docking Geometrically two molecules. POP: Optimal Partition (classification) QCM: Quantitative Chirality Measure of a conformer (graph automorphisms enumeration included) RADI: Computation of the Radius and Diameter of a spatial set. Molecular volume determines transport characteristics of molecules, such as intestinal absorption or blood-brain barrier penetration. Volume is therefore often used in QSAR studies to model molecular properties and biological activity. Various methods may be used to calculate molecular volume, including methods requiring generation of 3D molecular geometries, or fragment contribution methods such as McGowan volume approximation. | Tools for docking and small molecules by Dr. Michel Petitjean |
| LINK | ROCR (with obvious pronounciation) is an R package (http://www.r-project.org/) for evaluating and visualizing classifier performance. Currently, 28 performance measures are implemented, which can be freely combined to form parametric curves such as ROC curves, precision/recall curves, or lift curves. Many options such as curve averaging (for cross-validation or bootstrap), augmenting the averaged curves by standard error bar or boxplots, labeling cutoffs to the curve, or coloring curves according to cutoff. Tobias Sing, Oliver Sander, Niko Beerenwinkel, Thomas Lengauer. ROCR: visualizing classifier performance in R. Bioinformatics 21(20):3940-3941 (2005). See tutorials about ROC curve: http://www.anaesthetist.com/mnm/stats/roc/Findex.htm; http://nicolaorsini.altervista.org/stata/tutorial/r/tu_rocss.htm; http://pops.csse.monash.edu.au/roccurves_doc.html; http://www.mlahanas.de/MOEA/Med/ROC21.htm | Analyzing results of virtual screenings: ROC curves |
| CoLiBRI | Chemometric analysis of ligand receptor complementarity. Need to contact the authors, J Chem Inf Model 2006, 46, 844-851 | Fast reduction of the compound collection |
| LINK | Computes and manages molecular interaction fingerprints(i.e: between a ligand and a receptor) from the Rognan group and many others. Marcou, G. and Rognan, D. (2007) Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints J. Chem. Inf. Model., 47, 195-207 | Protein ligand interaction |
| LINK | PROFEAT- Protein Feature Server for computing physicochemical properties of proteins and peptides from their primary sequences. Z.R. Li, H.H. Lin, L.Y. Han, L. Jiang, X. Chen, and Y.Z. Chen. PROFEAT: A Web Server for Computing Structural and Physicochemical Features of Proteins and Peptides from Amino Acid Sequence. Nucleic Acids Res.Jul 1, 2006; 34(Web Server issue):W32-7. | PROFEAT- Protein Feature Server - SVM |
| LINK | ProtParam (References / Documentation) is a tool which allows the computation of various physical and chemical parameters for a given protein stored in Swiss-Prot or TrEMBL or for a user entered sequence. The computed parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY) | for SVM - protein parameter |
| Commonly used machine learning methods
Several machine learning (ML) methods have been widely used for the classification of pharmaceutical relevance. These include logistic regression (LR), linear discriminant analysis (LDA), k nearest neighbor (kNN), binary kernel discrimination (BKD), decision tree (DT), artificial neural network (ANN), probabilistic neural network (PNN) and support vector machines (SVMs). Websites for the freely downloadable codes of some methods are given in Table S1.
You have to copy and paste these ones:
DT PrecisionTree http://www.palisade.com.au/precisiontree/ DecisionPro http://www.vanguardsw.com/decisionpro/jdtree.htm C4.5 http://www2.cs.uregina.ca/~hamilton/courses/831/notes/ml/dtrees/c4.5/tutorial.html C5.0 http://www.rulequest.com/download.html kNN k Nearest Neighbor demo http://www.cs.cmu.edu/~zhuxj/courseproject/knndemo/KNN.html PERL Module for kNN http://aspn.activestate.com/ASPN/CodeDoc/AI-Categorize/AI/Categorize/kNN.html Java class for kNN http://nlp.stanford.edu/nlp/javadoc/javanlp/edu/stanford/nlp/classify/old/KNN.html Neural network BrainMaker http://www.calsci.com/ Neural network: JATOON http://www.dq.fct.unl.pt/staff/jas/qc/ Libneural http://pcrochat.online.fr/webus/tutorial/BPN_tutorial7.html Fann http://leenissen.dk/fann/ NeuralWorks Predict http://www.neuralware.com/products.jsp NeuroShell Predictor http://www.mbaware.com/neurpred.html SVMs SVM light http://svmlight.joachims.org/ LIBSVM http://www.csie.ntu.edu.tw/~cjlin/libsvm/ mySVM http://www-ai.cs.uni-dortmund.de/SOFTWARE/MYSVM/index.html SMO http://www.datalab.uci.edu/people/xge/svm/ BSVM http://www.csie.ntu.edu.tw/~cjlin/bsvm/ |
SVM, learning system | |
| LINK | I-interpret: uses standard geometry information about small ligands, like a ligand present in a PDB file and performs automatic atom/bond-type assignment. It can takes several compounds at a time and propose protonation state. See Zhao, Cheng and Wang, J Chem inf Model in press 2007. Title: automatic perception of organic molecules based on essential structural information | automatic atom/bond-type assignment for small ligand |
| LINK | Compute ligand-protein interaction energy after energy minimization performed by the package PLOP, protein local optimization program. See Jacobson et al, Proteins 2004, 55: 351-367 | Protein local optimization program, minimize ligands in pocket and compute energy |
| LINK | McMaster Canada, HTS-VLS competition | HTS-VLS competition |
| LINK | The Molecular Libraries Screening Centers Network (MLSCN) consists of 10 centers with a diverse set of screening platform technologies that include ultraHTS, cell based imaging, and flow cytometry.. NIH USA project on screening | NIH USA project on screening |
| LINK | Resources on bioinformatics classified by categories | Bioinformatics information |
| LINK | course chemoinformatics | training chemoinformatics |
| LINK | Kemo can help you find information about chemical compounds in the PubChem Compound database. | Chemoinformatics Artificial Intelligence |
| LINK | Alice: artificial intelligence foundation | Artificial Intelligence |
| LINK | This page provides an interface to our OWL-S/UDDI matchmaker. The interface provides you two functionality. First, you can create a OWL-S Profile of your web service and publish your webservice to the matchmaker. Second, you can create an OWL-S Profile describing the capabilities your are expecting in the soughted service, and submit the profile as a query to matchmaker. The interface is based on OWL-S 1.1 Profile. | Web service |
| LINK | SoftDB is a simple software database with a web interface designed to serve the needs of a particular field of research, in this case, structural biology. Since the scope of application is much more limited than similar systems such as freshmeat.net, the database and interface are relatively small, and can be run on almost any web server through the use of a few Perl scripts and a MySQL back-end database. | data flows (often referred to as pipelines) |
| LINK | KNIME, pronounced [naim], is a modular data exploration platform that enables the user to visually create data flows (often referred to as pipelines), selectively execute some or all analysis steps, and later investigate the results through interactive views on data and models. | data flows (often referred to as pipelines) |
| LINK | The Taverna project aims to provide a language and software tools to facilitate easy use of workflow and distributed compute technology within the eScience community | data flows (often referred to as pipelines) |
| LINK | A Graphical Workflow Composer for Web Services | Data flows (often referred to as pipelines) |
REF (many are in the tables above)
|
References for the Tables
Abagyan,
R., Lee, W.H., Raush, E., Budagyan, L., Totrov, M., Sundstrom, M., and
Marsden, B.D. 2006. Disseminating structural genomics data to the
public: from a data dump to an animated story. Trends Biochem Sci 31:
76-78.
Abagyan, R.A., Totrov, M., and Kuznetsov, D. 1994. ICM-a new method for protein modelling and design: Application to docking structure predictionfrom distorded native conformation. Journal of computational chemistry 15: 488-506. Ahmad, S., Kono, H., Arauzo-Bravo, M.J., and Sarai, A. 2006. ReadOut: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition. Nucleic Acids Res 34: W124-127. Ahmad, S., and Sarai, A. 2004. Qgrid: clustering tool for detecting charged and hydrophobic regions in proteins. Nucleic Acids Res 32: W104-107. Alland, C., Moreews, F., Boens, D., Carpentier, M., Chiusa, S., Lonquety, M., Renault, N., Wong, Y., Cantalloube, H., Chomilier, J., et al. 2005. RPBS: a web resource for structural bioinformatics. Nucleic Acids Res 33: W44-49. Ausiello, G., Cesareni, G., and Helmer-Citterich, M. 1997. ESCHER: a new docking procedure applied to the reconstruction of protein tertiary structure. Proteins 28: 556-567. Ausiello, G., Zanzoni, A., Peluso, D., Via, A., and Helmer-Citterich, M. 2005. pdbFun: mass selection and fast comparison of annotated PDB residues. Nucleic Acids Res 33: W133-137. Azuara, C., Lindahl, E., Koehl, P., Orland, H., and Delarue, M. 2006. PDB_Hydro: incorporating dipolar solvents with variable density in the Poisson-Boltzmann treatment of macromolecule electrostatics. Nucleic Acids Res 34: W38-42. Bader, G.D., Betel, D., and Hogue, C.W. 2003. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res 31: 248-250. Bagos, P.G., Liakopoulos, T.D., Spyropoulos, I.C., and Hamodrakas, S.J. 2004. PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins. Nucleic Acids Res 32: W400-404. Baker, N.A., Sept, D., Joseph, S., Holst, M.J., and McCammon, J.A. 2001. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad Sci U S A 98: 10037-10041. Bashford, D., and Karplus, M. 1990. pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. Biochemistry 29: 10219-10225. Bergner, A., Gunther, J., Hendlich, M., Klebe, G., and Verdonk, M. 2001. Use of Relibase for retrieving complex three-dimensional interaction patterns including crystallographic packing effects. Biopolymers 61: 99-110. Berjanskii, M.V., Neal, S., and Wishart, D.S. 2006. PREDITOR: a web server for predicting protein torsion angle restraints. Nucleic Acids Res 34: W63-69. Betzi, S., Suhre, K., Chetrit, B., Guerlesquin, F., and Morelli, X. 2006. GFscore: a general nonlinear consensus scoring function for high-throughput docking. J Chem Inf Model 46: 1704-1712. Binkowski, T.A., Adamian, L., and Liang, J. 2003. Inferring functional relationships of proteins from local sequence and spatial surface patterns. J Mol Biol 332: 505-526. Block, P., Sotriffer, C.A., Dramburg, I., and Klebe, G. 2006. AffinDB: a freely accessible database of affinities for protein-ligand complexes from the PDB. Nucleic Acids Res 34: D522-526. Bowie, J.U., Luthy, R., and Eisenberg, D. 1991. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253: 164-170. Brady, G.P., and Stouten, P.F.W. 2000. Fast prediction and visualization of protein binding pockets with PASS. J Computer-Aided Molecular Design 14: 383-401. Cai, C.Z., Han, L.Y., Ji, Z.L., Chen, X., and Chen, Y.Z. 2003. SVM-Prot: Web-based support vector machine software for functional classification of a protein from its primary sequence. Nucleic Acids Res 31: 3692-3697. Camacho, C.J., and Zhang, C. 2005. FastContact: rapid estimate of contact and binding free energies. Bioinformatics 21: 2534-2536. Canutescu, A.A., Shelenkov, A.A., and Dunbrack, R.L., Jr. 2003. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 12: 2001-2014. Chandonia, J.M., Hon, G., Walker, N.S., Lo Conte, L., Koehl, P., Levitt, M., and Brenner, S.E. 2004. The ASTRAL Compendium in 2004. Nucleic Acids Res 32: D189-192. Chang, D.T., Chen, C.Y., Chung, W.C., Oyang, Y.J., Juan, H.F., and Huang, H.C. 2004. ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures. Nucleic Acids Res 32: W76-82. Chang, D.T., Oyang, Y.J., and Lin, J.H. 2005. MEDock: a web server for efficient prediction of ligand binding sites based on a novel optimization algorithm. Nucleic Acids Res 33: W233-238. Chang, D.T., Weng, Y.Z., Lin, J.H., Hwang, M.J., and Oyang, Y.J. 2006. Protemot: prediction of protein binding sites with automatically extracted geometrical templates. Nucleic Acids Res 34: W303-309. Chang H and Fujita T. PicSNP: A Browsable Catalog of Nonsynonymous Single Nucleotide Polymorphisms in the Human Genome. Biochem. Biophys. Res. Commun. 287:288-291, 2001 Chelliah, V., Blundell, T.L., and Fernandez-Recio, J. 2006. Efficient restraints for protein-protein docking by comparison of observed amino acid substitution patterns with those predicted from local environment. J Mol Biol 357: 1669-1682. Chen, C.C., Hwang, J.K., and Yang, J.M. 2006. (PS)2: protein structure prediction server. Nucleic Acids Res 34: W152-157. Chen, R., Li, L., and Weng, Z. 2003. ZDOCK: an initial-stage protein-docking algorithm. Proteins 52: 80-87. Chen, X., Ji, Z.L., and Chen, Y.Z. 2002a. TTD: Therapeutic Target Database. Nucleic Acids Res 30: 412-415. Chen, X., Ji, Z.L., Zhi, D.G., and Chen, Y.Z. 2002b. CLiBE: a database of computed ligand binding energy for ligand-receptor complexes. Comput Chem 26: 661-666. Chen, X., Lin, Y., and Gilson, M.K. 2002c. The binding database. Biopolymers Nucleic Acid Sci 61: 127-142. Chen, X., and Reynolds, C.H. 2002. Performance of similarity measures in 2D fragment-based similarity searching: comparison of structural descriptors and similarity coefficients. J Chem Inf Comput Sci 42: 1407-1414. Claude, J.B., Suhre, K., Notredame, C., Claverie, J.M., and Abergel, C. 2004. CaspR: a web server for automated molecular replacement using homology modelling. Nucleic Acids Res 32: W606-609. Colovos, C., and Yeates, T.O. 1993. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 2: 1511-1519. Comeau, S.R., Gatchell, D.W., Vajda, S., and Camacho, C.J. 2004. ClusPro: a fully automated algorithm for protein-protein docking. Nucleic Acids Res 32: W96-99. Cruciani, G., Carosati, E., De Boeck, B., Ethirajulu, K., Mackie, C., Howe, T., and Vianello, R. 2005. MetaSite: understanding metabolism in human cytochromes from the perspective of the chemist. J Med Chem 48: 6970-6979. Daily, M.D., Masica, D., Sivasubramanian, A., Somarouthu, S., and Gray, J.J. 2005. CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock. Proteins 60: 181-186. Dalby, A., Nourse, J.G., Hounshell, W.D., Gushurst, A.K.I., Grier, D.L., Leland, B.A., and Laufer, J. 1992. Description of several chemical structure file formats used in computer programs developed at Molecular Design Limited. J Chem Inf Comput Sci 32: 244-255. Dantzer, J., Moad, C., Heiland, R., and Mooney, S. 2005. MutDB services: interactive structural analysis of mutation data. Nucleic Acids Res 33: W311-314. Davis, I.W., Murray, L.W., Richardson, J.S., and Richardson, D.C. 2004. MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res 32: W615-619. Deane, C.M., and Blundell, T.L. 2001. CODA: a combined algorithm for predicting the structurally variable regions of protein models. Protein Sci 10: 599-612. Delarue, M., and Sanejouand, Y.H. 2002. Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model. J Mol Biol 320: 1011-1024. Deshpande, N., Addess, K.J., Bluhm, W.F., Merino-Ott, J.C., Townsend-Merino, W., Zhang, Q., Knezevich, C., Xie, L., Chen, L., Feng, Z., et al. 2005. The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res 33: D233-237. DesJarlais, R.L., Sheridan, R.P., Seibel, G.L., Dixon, J.S., Kuntz, I.D., and Venkataraghavan, R. 1988. Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. J Med Chem 31: 722-729. Diemand, A.V., and Scheib, H. 2004. iMolTalk: an interactive, internet-based protein structure analysis server. Nucleic Acids Res 32: W512-516. Douguet, D., and Labesse, G. 2001. Easier threading through web-based comparisons and cross-validations. Bioinformatics 17: 752-753. Dundas, J., Ouyang, Z., Tseng, J., Binkowski, A., Turpaz, Y., and Liang, J. 2006. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res 34: W116-118. Ellis, L.B., Roe, D., and Wackett, L.P. 2006. The University of Minnesota Biocatalysis/Biodegradation Database: the first decade. Nucleic Acids Res 34: D517-521. Eyal, E., Najmanovich, R., Sobolev, V., and Edelman, M. 2001. MutaProt: a web interface for structural analysis of point mutations. Bioinformatics 17: 381-382. Fernandez-Fuentes, N., Zhai, J., and Fiser, A. 2006. ArchPRED: a template based loop structure prediction server. Nucleic Acids Res 34: W173-176. Fernandez-Recio J, Totrov M, Skorodumov C, Abagyan R. Optimal docking area: a new method for predicting protein-protein interaction sites. Proteins. 2005; 58:134-43. Ferrer-Costa, C., Gelpi, J.L., Zamakola, L., Parraga, I., de la Cruz, X., and Orozco, M. 2005. PMUT: a web-based tool for the annotation of pathological mutations on proteins. Bioinformatics 21: 3176-3178. Gabb, H.A., Jackson, R.M., and Sternberg, M.J. 1997. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 272: 106-120. Gabdoulline, R.R., Ulbrich, S., Richter, S., and Wade, R.C. 2006. ProSAT2--Protein Structure Annotation Server. Nucleic Acids Res 34: W79-83. Gabdoulline, R.R., Wade, R.C., and Walther, D. 1999. MolSurfer: two-dimensional maps for navigating three-dimensional structures of proteins. Trends Biochem Sci 24: 285-287. Gale, J.D. 1997. GULP - a computer program for the symmetry adapted simulation of solids. JCS Faraday Trans. 93: 629-637. Gautier, R., Camproux, A.C., and Tuffery, P. 2004. SCit: web tools for protein side chain conformation analysis. Nucleic Acids Res 32: W508-511. Gelly, J.C., Etchebest, C., Hazout, S., and de Brevern, A.G. 2006. Protein Peeling 2: a web server to convert protein structures into series of protein units. Nucleic Acids Res 34: W75-78. Girke, T., Cheng, L.C., and Raikhel, N. 2005. ChemMine. A compound mining database for chemical genomics. Plant Physiol 138: 573-577. Glaser, F., Pupko, T., Paz, I., Bell, R.E., Bechor-Shental, D., Martz, E., and Ben-Tal, N. 2003. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19: 163-164. Gold, N.D., and Jackson, R.M. 2006a. A searchable database for comparing protein-ligand binding sites for the analysis of structure-function relationships. J Chem Inf Model 46: 736-742. Gold, N.D., and Jackson, R.M. 2006b. SitesBase: a database for structure-based protein-ligand binding site comparisons. Nucleic Acids Res 34: D231-234. Sungsam Gong, Giseok Yoon, Insoo Jang, Dan Bolser, Panos Dafas, Michael Schroeder, Hansol Choi, Yoobok Cho, Kyungsook Han, Sunghoon Lee, Hwanho Choi, Michael Lappe, Liisa Holm, Sangsoo Kim, Donghoon Oh, Jonghwa Bhak. Bioinformatics. 2005 May 15;21:2541-3. Sungsam Gong, Changbum Park, Hansol Choi, Junsu Ko, Insoo Jang, Jungsul Lee, Dan M Bolser, Donghoon Oh, Deok-Soo Kim, Jong Bhak. A protein domain interaction interface database: InterPare. BMC Bioinformatics. 2005 Aug 25;6:207 Goodsell, D.S., Morris, G.M., and Olson, A.J. 1996. Automated docking of flexible ligands: applications of AutoDock. J Mol Recognit 9: 1-5. Gordon, J.C., Myers, J.B., Folta, T., Shoja, V., Heath, L.S., and Onufriev, A. 2005. H++: a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Res 33: W368-371. Grotthuss, v.M., Pas, J., and Rychlewski, L. 2003. Ligand-Info, searching for similar small compounds using index profiles. Bioinformatics 19: 1041-1042. Guerois, R., Nielsen, J.E., and Serrano, L. 2002. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J Mol Biol 320: 369-387. Guo, J.T., Ellrott, K., Chung, W.J., Xu, D., Passovets, S., and Xu, Y. 2004. PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction. Nucleic Acids Res 32: W522-525. Han, L.Y., Lin, H.H., Li, Z.R., Zheng, C.J., Cao, Z.W., Xie, B., and Chen, Y.Z. 2006. PEARLS: Program for Energetic Analysis of Receptor-Ligand System. J Chem Inf Model 46: 445-450. Hassinen, T., and Perakyla, M. 2001. New energy terms for reduced protein models implemented in an off-lattice force field. J Comp Chem 22: 1229-1242. Helma, C. 2006. Lazy structure-activity relationships (lazar) for the prediction of rodent carcinogenicity and Salmonella mutagenicity. Mol Divers. Hendlich, M. 1998. Databases for protein-ligand complexes. Acta Crystallogr D Biol Crystallogr 54: 1178-1182. Hendlich, M., Bergner, A., Gunther, J., and Klebe, G. 2003. Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions. J Mol Biol 326: 607-620. Hinsen, K. 2000. The molecular modelling toolkit: a new approach to molecular simulations. J. Comput. Chem. 21: 79-95. Hollup, S.M., Salensminde, G., and Reuter, N. 2005. WEBnm@: a web application for normal mode analyses of proteins. BMC Bioinformatics 6: 52. Humphrey, W., Dalke, A., and Schulten, K. 1996. VMD: visual molecular dynamics. J Mol Graph 14: 33-38, 27-38. Hung, J.H., Huang, H.D., and Lee, T.Y. 2006. ProKware: integrated software for presenting protein structural properties in protein tertiary structures. Nucleic Acids Res 34: W89-94. Irwin, J.J., and Shoichet, B.K. 2005. ZINC--a free database of commercially available compounds for virtual screening. J Chem Inf Model 45: 177-182. Jain, A.N. 2003. Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J Med Chem 46: 499-511. Jain, A.N. 2004. Ligand-based structural hypotheses for virtual screening. J Med Chem 47: 947-961. Jambon, M., Imberty, A., Deleage, G., and Geourjon, C. 2003. A new bioinformatic approach to detect common 3D sites in protein structures. Proteins 52: 137-145. Jang, Y., Jeong, J.I., and Kim, M.K. 2006. UMMS: constrained harmonic and anharmonic analyses of macromolecules based on elastic network models. Nucleic Acids Res 34: W57-62. Ji, Z.L., Han, L.Y., Yap, C.W., Sun, L.Z., Chen, X., and Chen, Y.Z. 2003. Drug Adverse Reaction Target Database (DART) : proteins related to adverse drug reactions. Drug Saf 26: 685-690. Kantardjiev, A.A., and Atanasov, B.P. 2006. PHEPS: web-based pH-dependent Protein Electrostatics Server. Nucleic Acids Res 34: W43-47. Kastenholz, M.A., Pastor, M., Cruciani, G., Haaksma, E.E., and Fox, T. 2000. GRID/CPCA: a new computational tool to design selective ligands. J Med Chem 43: 3033-3044. Katchalski-Katzir, E., Shariv, I., Eisenstein, M., Friesem, A.A., Aflalo, C., and Vakser, I.A. 1992. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci U S A 89: 2195-2199. Kellenberger, E., Muller, P., Schalon, C., Bret, G., Foata, N., and Rognan, D. 2006. sc-PDB: an Annotated Database of Druggable Binding Sites from the Protein Data Bank. J Chem Inf Model 46: 717-727. Kim, D.E., Chivian, D., and Baker, D. 2004. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res 32: W526-531. Kinoshita, K., Furui, J., and Nakamura, H. 2002. Identification of protein functions from a molecular surface database, eF-site. J Struct Funct Genomics 2: 9-22. Klekota, J., Roth, F.P., and Schreiber, S.L. 2006. Query Chem: a Google-powered web search combining text and chemical structures. Bioinformatics 22: 1670-1673. Kleywegt, G.J. 1999. Recognition of spatial motifs in protein structures. J Mol Biol 285: 1887-1897. Kleywegt, G.J., Harris, M.R., Zou, J.Y., Taylor, T.C., Wahlby, A., and Jones, T.A. 2004. The Uppsala Electron-Density Server. Acta Crystallogr D Biol Crystallogr 60: 2240-2249. Kleywegt, G.J., and Jones, T.A. 1994. Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr D Biol Crystallogr 50: 178-185. Koradi, R., Billeter, M., and Wuthrich, K. 1996. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph 14: 51-55, 29-32. Korb, O., Stutzle, T., and Exner, T.E. 2006. PLANTS: application of ant colony optimization to structure-based drug design. Ant Colony Optimization and Swarm Intelligence, 5th International Workshop: 247-258. Kraulis, P.J. 1991. MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures. J. Applied Crystallography 24: 946-950. Krieger, E., Koraimann, G., and Vriend, G. 2002. Increasing the precision of comparative models with YASARA NOVA--a self-parameterizing force field. Proteins 47: 393-402. Krieger, E., Nielsen, J.E., Spronk, C.A., and Vriend, G. 2006. Fast empirical pK(a) prediction by Ewald summation. J Mol Graph Model. Kundrotas, P.J., and Alexov, E. 2006. Electrostatic properties of protein-protein complexes. Biophys J 91: 1724-1736. Petras J Kundrotas, Emil Alexov. PROTCOM: searchable database of protein complexes enhanced with domain-domain structures. Nucleic Acids Res. 2006. Kuntz, I.D. 1992. Structure-based strategies for drug design and discovery. Science 257: 1078-1082. Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R., and Ferrin, T.E. 1982. A geometric approach to macromolecule-ligand interactions. J Mol Biol 161: 269-288. Laaksonen, L. 1992. A graphics program for the analysis and display of molecular dynamics trajectories. J. Mol. Graph. 10: 33-34. Laskowski, R.A. 1995. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph 13: 323-330, 307-328. Laskowski, R.A., Watson, J.D., and Thornton, J.M. 2005. ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 33: W89-93. Laurie, A.T., and Jackson, R.M. 2005. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 21: 1908-1916. Lee, S., Lee, B., Jang, I., Kim, S., and Bhak, J. 2006. Localizome: a server for identifying transmembrane topologies and TM helices of eukaryotic proteins utilizing domain information. Nucleic Acids Res 34: W99-W103. Lehtonen, J.V., Still, D.J., Rantanen, V.V., Ekholm, J., Bjorklund, D., Iftikhar, Z., Huhtala, M., Repo, S., Jussila, A., Jaakkola, J., et al. 2004. BODIL: a molecular modeling environment for structure-function analysis and drug design. J Comput Aided Mol Des 18: 401-419. Li, H., Gao, Z., Kang, L., Zhang, H., Yang, K., Yu, K., Luo, X., Zhu, W., Chen, K., Shen, J., et al. 2006. TarFisDock: a web server for identifying drug targets with docking approach. Nucleic Acids Res 34: W219-224. Li, H., Robertson, A.D., and Jensen, J.H. 2005. Very fast empirical prediction and rationalization of protein pKa values. Proteins 61: 704-721. Lindahl, E., Azuara, C., Koehl, P., and Delarue, M. 2006. NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res 34: W52-56. Linding, R., Jensen, L.J., Diella, F., Bork, P., Gibson, T.J., and Russell, R.B. 2003. Protein disorder prediction: implications for structural proteomics. Structure 11: 1453-1459. Liu, Y., and Kuhlman, B. 2006. RosettaDesign server for protein design. Nucleic Acids Res 34: W235-238. Magyar, C., Gromiha, M.M., Pujadas, G., Tusnady, G.E., and Simon, I. 2005. SRide: a server for identifying stabilizing residues in proteins. Nucleic Acids Res 33: W303-305. Mahe, P., Ueda, N., Akutsu, T., Perret, J.L., and Vert, J.P. 2005. Graph kernels for molecular structure-activity relationship analysis with support vector machines. J Chem Inf Model 45: 939-951. Mandell, J.G., Roberts, V.A., Pique, M.E., Kotlovyi, V., Mitchell, J.C., Nelson, E., Tsigelny, I., and Ten Eyck, L.F. 2001. Protein docking using continuum electrostatics and geometric fit. Protein Eng 14: 105-113. Martin, L., Catherinot, V., and Labesse, G. 2006. kinDOCK: a tool for comparative docking of protein kinase ligands. Nucleic Acids Res 34: W325-329. Massire, C., Gaspin, C., and Westhof, E. 1994. DRAWNA: a program for drawing schematic views of nucleic acids. J Mol Graph 12: 201-206, 196. Massire, C., and Westhof, E. 1998. MANIP: an interactive tool for modelling RNA. J Mol Graph Model 16: 197-205, 255-197. Maupetit, J., Gautier, R., and Tuffery, P. 2006. SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace. Nucleic Acids Res 34: W147-151. McGann, M.R., Almond, H.R., Nicholls, A., Grant, J.A., and Brown, F.K. 2003. Gaussian docking functions. Biopolymers 68: 76-90. McGuffin, L.J., Bryson, K., and Jones, D.T. 2000. The PSIPRED protein structure prediction server. Bioinformatics 16: 404-405. Michalsky, E., Dunkel, M., Goede, A., and Preissner, R. 2005. SuperLigands - a database of ligand structures derived from the Protein Data Bank. BMC Bioinformatics 6: 122. Miteva, M.A., Tuffery, P., and Villoutreix, B.O. 2005. PCE: web tools to compute protein continuum electrostatics. Nucleic Acids Res 33: W372-375. Miteva, M.A., Violas, S., Montes, M., Gomez, D., Tuffery, P., and Villoutreix, B.O. 2006. FAF-Drugs: Free ADME/tox Filtering of compound collections. Nucleic Acids Research 34: W738-744. Yoichi Murakami, Susan Jones. SHARP2: protein-protein interaction predictions using patch analysis. Bioinformatics. 2006 May 3 Nayal, M., Hitz, B.C., and Honig, B. 1999. GRASS: a server for the graphical representation and analysis of structures. Protein Sci 8: 676-679. Nayal, M., and Honig, B. 2006. On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites. Proteins. Neshich, G., Rocchia, W., Mancini, A.L., Yamagishi, M.E., Kuser, P.R., Fileto, R., Baudet, C., Pinto, I.P., Montagner, A.J., Palandrani, J.F., et al. 2004. JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure. Nucleic Acids Res 32: W595-601. Neuvirth H, Raz R, Schreiber G. ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol. 2004, 338(1):181-99. Ng, P.C., and Henikoff, S. 2003. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res 31: 3812-3814. Nissink, J.W., Murray, C., Hartshorn, M., Verdonk, M.L., Cole, J.C., and Taylor, R. 2002. A new test set for validating predictions of protein-ligand interaction. Proteins 49: 457-471. Ogmen, U., Keskin, O., Aytuna, A.S., Nussinov, R., and Gursoy, A. 2005. PRISM: protein interactions by structural matching. Nucleic Acids Res 33: W331-336. Paiardini, A., Bossa, F., and Pascarella, S. 2005. CAMPO, SCR_FIND and CHC_FIND: a suite of web tools for computational structural biology. Nucleic Acids Res 33: W50-55. Parthiban, V., Gromiha, M.M., and Schomburg, D. 2006. CUPSAT: prediction of protein stability upon point mutations. Nucleic Acids Res 34: W239-242. Pei, J., Wang, Q., Liu, Z., Li, Q., Yang, K., and Lai, L. 2006. PSI-DOCK: towards highly efficient and accurate flexible ligand docking. Proteins 62: 934-946. Petrey, D., Xiang, Z., Tang, C.L., Xie, L., Gimpelev, M., Mitros, T., Soto, C.S., Goldsmith-Fischman, S., Kernytsky, A., Schlessinger, A., et al. 2003. Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins 53 Suppl 6: 430-435. Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., and Ferrin, T.E. 2004. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem 25: 1605-1612. Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kale, L., and Schulten, K. 2005. Scalable molecular dynamics with NAMD. J Comput Chem 26: 1781-1802. Porter, C.T., Bartlett, G.J., and Thornton, J.M. 2004. The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 32: D129-133. Jaime Prilusky, Clifford E. Felder, Tzviya Zeev-Ben-Mordehai, Edwin Rydberg, Orna Man, Jacques S. Beckmann, Israel Silman, and Joel L. Sussman. FoldIndex: a simple tool to predict whether a given protein sequence is intrinsically unfolded. 2005, Bioinformatics. Pugalenthi, G., Shameer, K., Srinivasan, N., and Sowdhamini, R. 2006. HARMONY: a server for the assessment of protein structures. Nucleic Acids Res 34: W231-234. Pupko, T., Bell, R.E., Mayrose, I., Glaser, F., and Ben-Tal, N. 2002. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18 Suppl 1: S71-77. Ramensky, V., Bork, P., and Sunyaev, S. 2002. Human non-synonymous SNPs: server and survey. Nucleic Acids Res 30: 3894-3900. Raymer, M.L., Sanschagrin, P.C., Punch, W.F., Venkataraman, S., Goodman, E.D., and Kuhn, L.A. 1997. Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm. J Mol Biol 265: 445-464. Reumers J, Maurer-Stroh S, Schymkowitz J, Rousseau F. SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs. Bioinformatics. 2006 Sep 1;22(17):2183-5. Epub 2006 Jun 29. Richard, A.M., and Williams, C.R. 2002. Distributed structure-searchable toxicity (DSSTox) public database network: a proposal. Mutat Res 499: 27-52. Richard, A.M., Williams, C.R., and Cariello, N.F. 2002. Improving structure-linked access to publicly available chemical toxicity information. Curr Opin Drug Discov Devel 5: 136-143. Ritchie, D.W., and Kemp, G.J. 2000. Protein docking using spherical polar Fourier correlations. Proteins 39: 178-194. Rost, B., Yachdav, G., and Liu, J. 2004. The PredictProtein server. Nucleic Acids Res 32: W321-326. Ruan, J., Stormo, G.D., and Zhang, W. 2004. ILM: a web server for predicting RNA secondary structures with pseudoknots. Nucleic Acids Res 32: W146-149. Salerno, W.J., Seaver, S.M., Armstrong, B.R., and Radhakrishnan, I. 2004. MONSTER: inferring non-covalent interactions in macromolecular structures from atomic coordinate data. Nucleic Acids Res 32: W566-568. Sali, A., and Blundell, T.L. 1993. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234: 779-815. Samudrala, R., and Levitt, M. 2000. Decoys 'R' Us: a database of incorrect conformations to improve protein structure prediction. Protein Sci 9: 1399-1401. Sasin, J.M., and Bujnicki, J.M. 2004. COLORADO3D, a web server for the visual analysis of protein structures. Nucleic Acids Res 32: W586-589. Schlessinger, A., Yachdav, G., and Rost, B. 2006. PROFbval: predict flexible and rigid residues in proteins. Bioinformatics 22: 891-893. Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., and Wolfson, H.J. 2005. PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res 33: W363-367. Schuttelkopf, A.W., and van Aalten, D.M. 2004. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D Biol Crystallogr 60: 1355-1363. Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., and Serrano, L. 2005. The FoldX web server: an online force field. Nucleic Acids Res 33: W382-388. Shatsky, M., Dror, O., Schneidman-Duhovny, D., Nussinov, R., and Wolfson, H.J. 2004. BioInfo3D: a suite of tools for structural bioinformatics. Nucleic Acids Res 32: W503-507. Shih, E.S., Gan, R.C., and Hwang, M.J. 2006. OPAAS: a web server for optimal, permuted, and other alternative alignments of protein structures. Nucleic Acids Res 34: W95-98. Shulman-Peleg, A., Nussinov, R., and Wolfson, H.J. 2005. SiteEngines: recognition and comparison of binding sites and protein-protein interfaces. Nucleic Acids Res 33: W337-341. Shyu, C.R., Chi, P.H., Scott, G., and Xu, D. 2004. ProteinDBS: a real-time retrieval system for protein structure comparison. Nucleic Acids Res 32: W572-575. Sobolev, V., Eyal, E., Gerzon, S., Potapov, V., Babor, M., Prilusky, J., and Edelman, M. 2005. SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment. Nucleic Acids Res 33: W39-43. Sobolev, V., Moallem, T.M., Wade, R.C., Vriend, G., and Edelman, M. 1997. CASP2 molecular docking predictions with the LIGIN software. Proteins Suppl 1: 210-214. Soman, K.V., Midoro-Horiuti, T., Ferreon, J.C., Goldblum, R.M., Brooks, E.G., Kurosky, A., Braun, W., and Schein, C.H. 2000. Homology modeling and characterization of IgE binding epitopes of mountain cedar allergen Jun a 3. Biophys J 79: 1601-1609. Sotriffer, C.A., Gohlke, H., and Klebe, G. 2002. Docking into knowledge-based potential fields: a comparative evaluation of DrugScore. J Med Chem 45: 1967-1970. Springer, C., Adalsteinsson, H., Young, M.M., Kegelmeyer, P.W., and Roe, D.C. 2005. PostDOCK: a structural, empirical approach to scoring protein ligand complexes. J Med Chem 48: 6821-6831. Stahl, M.T. 2005. Open-source software: not quite endsville. Drug Discov Today 10: 219-222. Stark, A., Sunyaev, S., and Russell, R.B. 2003. A model for statistical significance of local similarities in structure. J Mol Biol 326: 1307-1316. Steinbeck, C. 2001. The automation of natural product structure elucidation. Curr Opin Drug Discov Devel 4: 338-342. Steinbeck, C., Hoppe, C., Kuhn, S., Floris, M., Guha, R., and Willighagen, E.L. 2006. Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics. Curr. Pharm. Des. 12: 2111-2120. Steinbeck, C., Krause, S., and Kuhn, S. 2003. NMRShiftDB-constructing a free chemical information system with open-source components. J Chem Inf Comput Sci 43: 1733-1739. Steinbeck, C., and Kuhn, S. 2004. NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database. Phytochemistry 65: 2711-2717. Stitziel NO, Tseng YY, Pervouchine D, Goddeau D, Kasif S, Liang J. Structural location of disease-associated single-nucleotide polymorphisms. J Mol Biol. 2003, 327:1021-30 Sun, L.Z., Ji, Z.L., Chen, X., Wang, J.F., and Chen, Y.Z. 2002. ADME-AP: a database of ADME associated proteins. Bioinformatics 18: 1699-1700. Tetko, I.V., and Tanchuk, V.Y. 2002. Application of associative neural networks for prediction of lipophilicity in ALOGPS 2.1 program. J Chem Inf Comput Sci 42: 1136-1145. Joan Teyra, Andreas Doms, Michael Schroeder, M Teresa Pisabarro. SCOWLP: a web-based database for detailed characterization and visualization of protein interfaces. BMC Bioinformatics. 2006. Thomas, R.S., Rank, D.R., Penn, S.G., Craven, M.W., Drinkwater, N.R., and Bradfield, C.A. 2002. Developing toxicologically predictive gene sets using cDNA microarrays and Bayesian classification. Methods Enzymol 357: 198-205. Torda, A.E., Procter, J.B., and Huber, T. 2004. Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices. Nucleic Acids Res 32: W532-535. Toseland, C.P., McSparron, H., Davies, M.N., and Flower, D.R. 2006. PPD v1.0--an integrated, web-accessible database of experimentally determined protein pKa values. Nucleic Acids Res 34: D199-203. Tovchigrechko, A., and Vakser, I.A. 2006. GRAMM-X public web server for protein-protein docking. Nucleic Acids Res 34: W310-314. Trepalin, S.V., Yarkov, A.V., Pletnev, I.V., and Gakh, A.A. 2006. A Java Chemical Structure Editor Supporting the Modular Chemical Descriptor Language (MCDL). Molecules 11: 219-231. Tsuchiya, Y., Kinoshita, K., Ito, N., and Nakamura, H. 2006. PreBI: prediction of biological interfaces of proteins in crystals. Nucleic Acids Res 34: W20-24. Tyagi, M., Sharma, P., Swamy, C.S., Cadet, F., Srinivasan, N., de Brevern, A.G., and Offmann, B. 2006. Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet. Nucleic Acids Res 34: W119-123. Tynan-Connolly, B.M., and Nielsen, J.E. 2006. pKD: re-designing protein pKa values. Nucleic Acids Res 34: W48-51. van Aalten, D.M., Bywater, R., Findlay, J.B., Hendlich, M., Hooft, R.W., and Vriend, G. 1996. PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J Comput Aided Mol Des 10: 255-262. Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A.E., and Berendsen, H.J.C. 2005. GROMACS: fast, flexible and free. J Comput Chem 26: 1701-1718. Vaque, M., Arola, A., Aliagas, C., and Pujadas, G. 2006. BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock. Bioinformatics 22: 1803-1804. Verdonk, M.L., Cole, J.C., Watson, P., Gillet, V., and Willett, P. 2001. SuperStar: improved knowledge-based interaction fields for protein binding sites. J Mol Biol 307: 841-859. von Freyberg, B., Richmond, T.J., and Braun, W. 1993. Surface area included in energy refinement of proteins. A comparative study on atomic solvation parameters. J Mol Biol 233: 275-292. Vriend, G. 1990. WHAT IF: a molecular modeling and drug design program. J Mol Graph 8: 52-56, 29. Waldispuhl, J., Berger, B., Clote, P., and Steyaert, J.M. 2006. transFold: a web server for predicting the structure and residue contacts of transmembrane beta-barrels. Nucleic Acids Res 34: W189-193. Wang, R., Fang, X., Lu, Y., Yang, C.Y., and Wang, S. 2005. The PDBbind database: methodologies and updates. J Med Chem 48: 4111-4119. Wang, R., Gao, Y., and Lai, L. 2000a. Calculating partition coefficient by atom-additive method. Perspectives in Drug Discovery and Design 19: 47-66. Wang, R., Gao, Y., and Lai, L. 2000b. LigBuilder: a multiple-purpose program for structure-based drug design. J Mol Mod 6: 498-516. Wang, R., Lai, L., and Wang, S. 2002a. Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J Comput Aided Mol Des 16: 11-26. Wang, R., Liu, L., Lai, L., and Tang, Y. 1998. SCORE: A New Empirical Method for Estimating the Binding Affinity of a Protein-Ligand Complex. J. Mol. Modeling 4: 379-394. Wang, T., and Zhou, J. 1999. 3DFS: 3D Flexible Searching System for Lead Discovery – New Version 1.2. J Mol Mod 5: 231-251. Wang, Y., Anderson, J.B., Chen, J., Geer, L.Y., He, S., Hurwitz, D.I., Liebert, C.A., Madej, T., Marchler, G.H., Marchler-Bauer, A., et al. 2002b. MMDB: Entrez's 3D-structure database. Nucleic Acids Res 30: 249-252. Ward, J.J., Sodhi, J.S., McGuffin, L.J., Buxton, B.F., and Jones, D.T. 2004. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 337: 635-645. Wernersson, R., Rapacki, K., Staerfeldt, H.H., Sackett, P.W., and Molgaard, A. 2006. FeatureMap3D--a tool to map protein features and sequence conservation onto homologous structures in the PDB. Nucleic Acids Res 34: W84-88. Christof Winter, Andreas Henschel, Wan Kyu Kim, Michael Schroeder. SCOPPI: a structural classification of protein-protein interfaces. Nucleic Acids Res. 2006 Jan 1;34:D310-4 Wishart, D.S., Knox, C., Guo, A.C., Shrivastava, S., Hassanali, M., Stothard, P., Chang, Z., and Woolsey, J. 2006. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res 34: D668-672. Xenarios, I., Salwinski, L., Duan, X.J., Higney, P., Kim, S.M., and Eisenberg, D. 2002. DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res 30: 303-305. Yang, L.W., Rader, A.J., Liu, X., Jursa, C.J., Chen, S.C., Karimi, H.A., and Bahar, I. 2006. oGNM: online computation of structural dynamics using the Gaussian Network Model. Nucleic Acids Res 34: W24-31. Ye, Y., and Godzik, A. 2004. FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res 32: W582-585. Ying, X., Luo, H., Luo, J., and Li, W. 2004. RDfolder: a web server for prediction of RNA secondary structure. Nucleic Acids Res 32: W150-153. Yue P, Melamud E, Moult J. SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics 2006, 22:166 Zanzoni, A., Montecchi-Palazzi, L., Quondam, M., Ausiello, G., Helmer-Citterich, M., and Cesareni, G. 2002. MINT: a Molecular INTeraction database. FEBS Lett 513: 135-140. Zhang, J., Aizawa, M., Amari, S., Iwasawa, Y., Nakano, T., and Nakata, K. 2004. Development of KiBank, a database supporting structure-based drug design. Comput Biol Chem 28: 401-407. Zheng, C.J., Zhou, H., Xie, B., Han, L.Y., Yap, C.W., and Chen, Y.Z. 2004. TRMP: a database of therapeutically relevant multiple pathways. Bioinformatics 20: 2236-2241. Zsoldos, Z., Reid, D., Simon, A., Sadjad, S.B., and Johnson, A.P. 2006. eHiTS: an innovative approach to the docking and scoring function problems. Curr Protein Pept Sci. 7:421-435. |