Villoutreix Links: Free Structural Bioinformatics and VLS tools

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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.
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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.
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Free computer tools in Structural Bioinformatics and Chemoinformatics Optimized for Firefox
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)

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
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 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

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

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