1 | SIGMA-ALDRICH http://www.sigmaaldrich.com/life-science/molecular-biology/molecular-biology-products.html?TablePage=103192872 | Ready to order Bioactive small molecules for epigenetic research. |
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2 | SuperDrug Database http://bioinf.charite.de/superdrug/ | Contains around 2500 3D-structures of active ingredients of essential marketed drugs. |
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3 | ChemMine tools http://chemmine.ucr.edu/ | An online service for analyzing and clustering small molecules based on structural similarities, physicochemical properties or custom data types. |
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4 | Chemspider http://www.chemspider.com/ | Chemical structure database furnishing fast text and structure search access to over 26 million structures from hundreds of data sources. |
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5 | TTD- Therapeutics Target Database http://bidd.nus.edu.sg/group/ttd/ttd.asp | Database of cognized and explored protein and nucleic acid targets, targeted disease, fitting drugs directed at each of these targets. |
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6 | PubChem http://pubchem.ncbi.nlm.nih.gov/ | Database of chemical compounds along with bioassay results. |
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7 | DrugBank http://www.drugbank.ca/ | Bioinformatics and cheminformatics resource combining detailed drug data with comprehensive drug target information. |
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8 | ChEBI- Chemical Entities of Biological Interest http://www.ebi.ac.uk/chebi/ | Dictionary of molecular entities focused on small molecules. |
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9 | PDBeChem http://www.ebi.ac.uk/pdbe-srv/pdbechem/ | Dictionary of ligands, small molecules and monomers cited in PDB entries and maintained by the wwPDB. |
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10 | KEGG Drugs http://www.genome.jp/kegg/drug/ | Comprehensive drug information resource for approved drugs in Japan, USA, and Europe. |
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11 | e-Drug3D http://chemoinfo.ipmc.cnrs.fr/MOLDB/index.html | Database reflecting the current content of the U.S. pharmacopeia of small drugs. |
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12 | DNP- Dictionary of Natural Products http://dnp.chemnetbase.com/intro/index.jsp | Detailed and fully-edited database on natural products, originating from the Dictionary of Organic Compounds (DOC). |
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13 | ChemIDPlus http://chem.sis.nlm.nih.gov/chemidplus/ | Database of compounds and structures. |
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14 | eMolecules tool http://www.emolecules.com/ | Database of unique molecules. |
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15 | CTD- Comparative Toxicogenomics Database http://ctdbase.org/ | Database describing cross-species chemical-gene/protein interactions and chemical and gene disease relationships to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases with manually curated data. |
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16 | Ligand.Info http://ligand.info/ | Small-Molecule Meta-Database, compilation of various freely available databases of small molecules such as ChemBank, ChemPDB, KEGG, NCI, AKos GmbH, Asinex Ltd, and TimTec. |
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17 | CSD- Cambridge Structural Database http://www.ccdc.cam.ac.uk/products/csd/ | Small molecule crystal structures repository (in CIF format). |
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18 | SwissDock http://swissdock.vital-it.ch/ | Web service for predicting molecular interaction possible between small molecule and target protein. |
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19 | DUD.E. - Database of Useful Decoys: Enhanced http://dude.docking.org/ | Enhanced database, which helps to test docking algorithms by providing challenging decoys. |
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20 | BindingDB - the binding database http://www.bindingdb.org/bind/index.jsp | database of measured binding affinities emphasising chiefly on the interaction of the protein considered to be drug targets with small molecule, drug-like molecule. |
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21 | TarFisDock - Target Fishing Dock http://www.dddc.ac.cn/tarfisdock/ | a web server for identifying drug targets with docking approach |
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22 | PharmMapper http://59.78.96.61/pharmmapper/ | a web server for potential drug target identification using pharmacophore mapping approach. |
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23 | PRODRG - The GlycoBioChem PRODRG server http://davapc1.bioch.dundee.ac.uk/prodrg/ | Input is a short description of small molecule and the outputs are varieties of topologies, which can be utilized by mutiple programs along with energy minimized coordinates. |
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24 | DoD - Dictionary of drugs (Pharmasource formerly) http://dod.chemnetbase.com/tour/ | Resource for medicinal and pharmaceutical chemists with over 40000 pharmacologically active compound. |
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25 | ChEMBL https://www.ebi.ac.uk/chembl/# | Database of bioactive small molecules (drug-like molecules) containing 2-D structures, calculated properties and abstracted bioactivities. |
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26 | EuroCarbDB http://www.ebi.ac.uk/eurocarb/home.action | Database with structures of carbohydrates and experimental data. |
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27 | ZINC Database http://zinc.docking.org/ | Collection of curated commercially available chemical compounds proposed especially for virtual screening and differs from other chemical databases in its biologically relevent, 3D representation. |
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28 | ChemBank http://chembank.broadinstitute.org/ | Platform for studying data, which includes freely available data derived from small molecules and small-molecule screens, and resources. |
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29 | WOMBAT- World of molecular bioactivity http://www.sunsetmolecular.com/index.php?option=com_content&view=article&id=23&Itemid=1 | Database of several entries, representing some unique targets with bioactivity annotations. |
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30 | Virtual library Repository http://www2.nbcr.net/data/sw/hosted/virtuallib/ | Libraries of 30,184 (redundant) and 4,544 small-molecule fragments, all less than 150 daltons in weight, derived from FDA-approved compounds using the python script fragmentizer. |
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31 | Glide Fragment Library http://www.schrodinger.com/productpage/14/5/73/ | A0Set of 441 unique small fragments derived from molecules in the medicinal chemistry literature. |
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32 | ChemDB/ChemicalSearch http://cdb.ics.uci.edu/cgibin/ChemicalSearchWeb.py | Chemical search facility by various parameters. |
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33 | SPRESIweb http://www.spresi.com/ | The largest database of organic chemistry worldwide integrating over 8.7 million molecules, 4.1 million of reactions, references and 164000 patents covering the years 1974 - 2010. |
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34 | T3DB- Toxin, Toxin Target Database http://www.t3db.org/ | Database of common toxins as well as associated toxin targets. |
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35 | TCM- Traditional Chinese Medicine Database http://tcm.cmu.edu.tw/ | Small molecular database on traditional Chinese medicine for virtual screening. |
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36 | BitterDB- bitter database http://bitterdb.agri.huji.ac.il/bitterdb/ | Database of bitter compounds. |
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37 | Hit2Lead- ChemBridge online chemical store https://www.hit2lead.com/ | Commercial screening of small molecules. |
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38 | MUV- Maximum Unbiased Validation http://www.pharmchem.tu-bs.de/lehre/baumann/MUV.html | Datasets for Virtual Screening, with non-clumpy, spatially random topology. |
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39 | NRDBSM- Non Redundant Database of Small Molecules http://www.scfbio-iitd.res.in/software/nrdbsm/index.jsp | Aimed at virtual high throughput screening of small molecules and their further optimization into successful lead-like candidates. |
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40 | Superligands http://bioinf-tomcat.charite.de/superligands/ | Database with ligand oriented view of the protein structural space. Contains small molecules, which occur as ligands in the PDB. |
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41 | Ligand Expo (formerly ligand depot) http://ligand-depot.rutgers.edu/index.html | Provides chemical and structural information about small molecules within the structure entries of the Protein Data Bank. |
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42 | GLIDA - GPCR-Ligand Database http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/ | Renders information on both GPCRs and their known ligands. Query can be made either by GPCR search or ligand search. |
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43 | Glide Ligand Decoys Set http://www.schrodinger.com/productpage/14/5/74/ | Collection created by selecting 1000 ligands from a one million compound library that were chosen to exhibit "drug-like" properties. Used in Glide enrichment studies. |
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44 | S3DB - Simple Sloppy Semantic Database http://www.s3db.org/ | Database with manually curated structures of ligand and targets. |
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45 | DUD. - Directory of Useful Decoys http://dud.docking.org/ | Helps to test docking algorithms by providing challenging decoys. |
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46 | wwLigCSRre - ligand similarity search http://bioserv.rpbs.univ-paris-diderot.fr/Help/wwLigCSRre.html | it is designated for searching banks for compounds similar to a query, based on both coordinates and physico-chemical properties of atoms. |
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47 | RESID http://www.ebi.ac.uk/RESID/ | comprehensive collection of annotations and structures for protein modifications. |
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48 | the druggable genome database http://www.sophicalliance.com/services%20drug%20genome.php | Aims to provide a single repository of druggable genes that will support a wide range of cancer research initiatives. |
| | URL not working as on 10 Feb 2015 (confirmed on 15 Nov 2016) |
49 | SwissSideChain http://swisssidechain.ch/ | Structural and molecular mechanism database of many non-natural amino acid sidechains, which can be used to understand their insertion into natural proteins. |
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50 | SwissParam http://swissparam.ch/ | This service provides topology and parameters for small organic molecules compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS. |
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51 | SLITHER http://slither.rcas.sinica.edu.tw/ | A web server, which generates contiguous conformations of substrate molecules entering into deep active sites of protein or migrating across membrane transporters.
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