Free computer tools in Structural Bioinformatics and Chemoinformatics
We believe in the right balance between commercial and free computer packages
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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 for new links, questions, critics, please contact us


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

 Summary (PDF here)

In today's research environment, a wealth of experimental/theoretical structural data are available and the number of therapeutically relevant macromolecular structures is growing rapidly. This, coupled with the huge number of small non-peptide potential drug candidates easily available (over 7 million compounds), highlight the need of using computer-aided techniques for the efficient identification and optimization of novel hit compounds. Virtual (or in silico) ligand screening based on the three-dimensional structure of macromolecular targets (SB-VLS) is firmly established as an important approach to identify chemical entities that have a high likelihood of binding to a target molecule to elicit desired biological responses. A myriad of free applications and services facilitating the drug discovery process have been posted on the Web. This review mentions URLs that are useful for SB-VLS projects and essentially free for academic groups. We attempt to provide links for in silico ADME/tox prediction tools, compound collections, some ligand-based methods, characterization/simulation of 3D targets and homology modeling tools, druggable pocket predictions, active site comparisons, analysis of macromolecular interfaces, protein docking tools to help identify binding pockets and protein-ligand docking/scoring methods. As such, we aim at providing both, methods pertaining to the field of Structural Bioinformatics (defined here as tools to study macromolecules) and methods pertaining to the field of Chemoinformatics (defined here as tools to make better decisions faster in the arena of drug/lead identification and optimization). We also report several recent success stories using these free computer methods. This review should help readers finding free computer tools useful for their projects. Overall, we are confident that these tools will facilitate rapid and cost-effective identification of new hit compounds. The URLs presented in this review will be updated regularly at www.vls3d.com in the coming months, Links section.




Table I: Patent search

LINK

LINK

LINK

LINK

LINK

LINK

LINK

LINK

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 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 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

LINK

LINK

 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

LINK

LINK

 Computational chemistry package Chemistry tools
LINK

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

LINK

LINK

 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

LINK

LINK

 GDIS is a program for the display and manipulation of isolated molecules and periodic systems Molecular graphics

LINK

LINK

 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 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



Table III: ADME/tox prediction and some related databases

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 FAF-Drugs: ADME/tox online (Miteva et al. 2006) 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 Toxicoinformatics database at the FDA (application of systems biology to ADME/Tox) 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) 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 FDA approved drugs Drugs
LINK ChemBank: Free collections and utilities, known drugs, many annotated molecules, molecules with druglike and non-druglike properties Compound Database, Compound searching
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 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 (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.) ADME/Tox
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 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 DrugBank: Numerous data about drugs and targets including drugs already in use (Wishart et al. 2006) Compound Database, Macromolecules
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 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
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 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. AurŽlienÊMonge, 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-