Small molecules

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.

SuperDrug Database
http://bioinf.charite.de/superdrug/

Contains around 2500 3D-structures of active ingredients of essential marketed drugs.

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.

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.

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.

PubChem
http://pubchem.ncbi.nlm.nih.gov/

Database of chemical compounds along with bioassay results.

DrugBank
http://www.drugbank.ca/

Bioinformatics and cheminformatics resource combining detailed drug data with comprehensive drug target information.

ChEBI- Chemical Entities of Biological Interest
http://www.ebi.ac.uk/chebi/

Dictionary of molecular entities focused on small molecules.

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.

KEGG Drugs
http://www.genome.jp/kegg/drug/

Comprehensive drug information resource for approved drugs in Japan, USA, and Europe.

e-Drug3D
http://chemoinfo.ipmc.cnrs.fr/MOLDB/index.html

Database reflecting the current content of the U.S. pharmacopeia of small drugs.

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).

ChemIDPlus
http://chem.sis.nlm.nih.gov/chemidplus/

Database of compounds and structures.

eMolecules tool
http://www.emolecules.com/

Database of unique molecules.

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.

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.

CSD- Cambridge Structural Database
http://www.ccdc.cam.ac.uk/products/csd/

Small molecule crystal structures repository (in CIF format).

SwissDock
http://swissdock.vital-it.ch/

Web service for predicting molecular interaction possible between small molecule and target protein.

DUD.E. - Database of Useful Decoys: Enhanced
http://dude.docking.org/

Enhanced database, which helps to test docking algorithms by providing challenging decoys.

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.

TarFisDock - Target Fishing Dock
http://www.dddc.ac.cn/tarfisdock/

a web server for identifying drug targets with docking approach

PharmMapper
http://59.78.96.61/pharmmapper/

a web server for potential drug target identification using pharmacophore mapping approach.

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.

DoD - Dictionary of drugs (Pharmasource formerly)
http://dod.chemnetbase.com/tour/

Resource for medicinal and pharmaceutical chemists with over 40000 pharmacologically active compound.

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/

A0Set 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

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.

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