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Created on: 16-Sep-2012   Last updated on: 06-Oct-2012  |  How to cite this?
Total resources - 51
A list of resources for small molecules
Akhil Patel (Correspondence: Acharya KK, kshitish@ibab.ac.in)

Resources
Short description*Rank by usage frequency Click to Edit / Add comments
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.
1
SuperDrug Database
http://bioinf.charite.de/superdrug/
Contains around 2500 3D-structures of active ingredients of essential marketed drugs.
50
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.
50
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.
50
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.
67
PubChem
http://pubchem.ncbi.nlm.nih.gov/
Database of chemical compounds along with bioassay results.
82
DrugBank
http://www.drugbank.ca/
Bioinformatics and cheminformatics resource combining detailed drug data with comprehensive drug target information.
83
ChEBI- Chemical Entities of Biological Interest
http://www.ebi.ac.uk/chebi/
Dictionary of molecular entities focused on small molecules.
84
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.
84
KEGG Drugs
http://www.genome.jp/kegg/drug/
Comprehensive drug information resource for approved drugs in Japan, USA, and Europe.
84
e-Drug3D
http://chemoinfo.ipmc.cnrs.fr/MOLDB/index.html
Database reflecting the current content of the U.S. pharmacopeia of small drugs.
84
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).
84
ChemIDPlus
http://chem.sis.nlm.nih.gov/chemidplus/
Database of compounds and structures.
84
eMolecules tool
http://www.emolecules.com/
Database of unique molecules.
84
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.
84
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.
84
CSD- Cambridge Structural Database
http://www.ccdc.cam.ac.uk/products/csd/
Small molecule crystal structures repository (in CIF format).
84
SwissDock
http://swissdock.vital-it.ch/
Web service for predicting molecular interaction possible between small molecule and target protein.
84
DUD.E. - Database of Useful Decoys: Enhanced
http://dude.docking.org/
Enhanced database, which helps to test docking algorithms by providing challenging decoys.
84
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.
84
TarFisDock - Target Fishing Dock
http://www.dddc.ac.cn/tarfisdock/
a web server for identifying drug targets with docking approach
84
PharmMapper
http://59.78.96.61/pharmmapper/
a web server for potential drug target identification using pharmacophore mapping approach.
84
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.
84
DoD - Dictionary of drugs (Pharmasource formerly)
http://dod.chemnetbase.com/tour/
Resource for medicinal and pharmaceutical chemists with over 40000 pharmacologically active compound.
97
ChEMBL
https://www.ebi.ac.uk/chembl/#
Database of bioactive small molecules (drug-like molecules) containing 2-D structures, calculated properties and abstracted bioactivities.
100
EuroCarbDB
http://www.ebi.ac.uk/eurocarb/home.action
Database with structures of carbohydrates and experimental data.
100
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.
100
ChemBank
http://chembank.broadinstitute.org/
Platform for studying data, which includes freely available data derived from small molecules and small-molecule screens, and resources.
100
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.
100
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.
100
Glide Fragment Library
http://www.schrodinger.com/productpage/14/5/73/
 Set of 441 unique small fragments derived from molecules in the medicinal chemistry literature.
100
ChemDB/ChemicalSearch
http://cdb.ics.uci.edu/cgibin/ChemicalSearchWeb.py
Chemical search facility by various parameters.
100
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.
100
T3DB- Toxin, Toxin Target Database
http://www.t3db.org/
Database of common toxins as well as associated toxin targets.
100
TCM- Traditional Chinese Medicine Database
http://tcm.cmu.edu.tw/
Small molecular database on traditional Chinese medicine for virtual screening.
100
BitterDB- bitter database
http://bitterdb.agri.huji.ac.il/bitterdb/
Database of bitter compounds.
100
Hit2Lead- ChemBridge online chemical store
https://www.hit2lead.com/
Commercial screening of small molecules.
100
MUV- Maximum Unbiased Validation
http://www.pharmchem.tu-bs.de/lehre/baumann/MUV.html
Datasets for Virtual Screening, with non-clumpy, spatially random topology.
100
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.
100
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.
100
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.
100
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.
100
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.
100
S3DB - Simple Sloppy Semantic Database
http://www.s3db.org/
Database with manually curated structures of ligand and targets.
100
DUD. - Directory of Useful Decoys
http://dud.docking.org/
Helps to test docking algorithms by providing challenging decoys.
100
it is designated for searching banks for compounds similar to a query, based on both coordinates and physico-chemical properties of atoms.
100
RESID
http://www.ebi.ac.uk/RESID/
comprehensive collection of annotations and structures for protein modifications.
100
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.
100

URL not working as on 10 Feb 2015 (confirmed on 15 Nov 2016)
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.
100
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.
100
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.
100
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