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click2drug swissdock swissparam swisssidechain swissbioisostere swisstargetprediction about us swiss institute of bioinformatics click2drug disclaimer contacts citations encyclopedia chemistry hydrocarbons heterocycles must know functional groups frequent rings in fda frequent scaffolds in fda bibliography last additions general all docking all methodology scoring functions benchmarks web services reviews screening all methodology / all meth. / structure-based meth. / ligand-based benchmarks web services reviews target prediction all binding site prediction all methodology web services reviews ligand design all methodology web services reviews physico-chemical properties logp visualization all reviews directory directory of tools all databases chemical structure representations molecular modeling homology modeling binding site prediction docking screening ligand design binding free energy estimation qsar adme toxicity mobile applications last additions tag cloud faq directory of tools databases chemical structure rep. molecular modeling homology modeling binding site prediction docking screening target prediction ligand design binding free energy estimation qsar adme toxicity mobile applications last additions tag cloud faq directory of computer-aided drug design tools click2drug contains a comprehensive list of computer-aided drug design (cadd) software, databases and web services. these tools are classified according to their application field, trying to cover the whole drug design pipeline. if you think that an interesting tool is missing in this list, please contact us. updated on 4/5/2018. currently 807 links. show all links / hide all links . click on the following picture to select tools related to a given activity: show all links hide all links databases zincdatabase , zinc15database , chembl , bingo , jchemforexcel , chemdiff , proteindatabank(pdb) , bindingmoad(motherofalldatabase) , pdbbind , ttd , stitch , smpdb , ... chemical databases zinc database . curated collection of commercially available chemical compounds, with 3d coordinates, provided by the shoichet laboratory in the department of pharmaceutical chemistry at the university of california, san francisco (ucsf). zinc15 database . a new version of zinc database including 100+ million purchasable compounds in ready-to-dock, 3d formats, provided by the shoichet laboratory in the department of pharmaceutical chemistry at the university of california, san francisco (ucsf). chembl . curated database of small molecules. includes interactions and functional effects of small molecules binding to their macromolecular targets, and series of drug discovery databases. chemspider . collection of chemical compunds maintained by the royal society of chemistry. includes the conversion of chemical names to chemical structures, the generation of smiles and inchi strings as well as the prediction of many physicochemical parameters. cococo . free suite of multiconformational molecular databases for high-throughput virtual screening. it has single and multi conformer databases prepared for htvs in different formats like phase, catalyst, unity and sdf. provided by the department of pharmaceutical sciences of the university of modena and reggio emilia. drugbank . bioinformatics and cheminformatics resource combining detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. allows searching for similar compounds. pubchem . database of chemical compounds maintained by the national center for biotechnology information (ncbi), along with bioassays results. allows similar compounds search (2d and 3d). tcm . free small molecular database on traditional chinese medicine, for virtual screening. it is currently the world's largest tcm database, and contains 170'000 compounds, with 3d mol2 and 2d cdx files, which passed admet filters. scubidoo . a freely accessible database concept that currently holds 21 million virtual products originating from a small library of building blocks and a collection of robust organic reactions. this large data set was reduced to three representative and computationally tractable samples denoted as s, m, and l, containing 9994, 99 977, and 999 794 products, respectively. these small sets are useful as starting points for ligand identification and optimization projects. proposed by the university of university of marburg, germany. mcule database . commercial database of commercially available small molecules. allows filtering by chemical supplier data (stock availability, price, delivery time, chemical suppliers, catalogs, minimum purity, etc.) and export the whole mcule database including supplier and procurement related properties. reduced prices for academic. provided by mcule. wombat . (world of molecular bioactivity). database of 331,872 entries (268,246 unique smiles), representing 1,966 unique targets, with bioactivity annotations. compiled by sunset molecular discovery llc. approved drugs . the approved drugs app contains over a thousand chemical structures and names of small molecule drugs approved by the us food & drug administration (fda). structures and names can be browsed in a list, searched by name, filtered by structural features, and ranked by similarity to a user-drawn structure. the detail view allows viewing of a 3d conformation as well as tautomers. structures can be exported in a variety of ways, e.g. email, twitter, clipboard. for ipad and iphone. developed by molecular materials informatics, inc. chemspider mobile . allows searching the chemspider chemical database, provided by the royal society of chemistry. compounds can be searched by structure or by name, and browsed within the app. results can be examined by jumping to the web page. search structures are drawn using the powerful mmds molecular diagram editor. for ipad. provided by molecular materials informatics, inc. e-drug3d . database mirroring the current content of the u.s. pharmacopeia of small drugs. contains 1822 molecular structures with a molecular weight < 2000 (last update: july 2016). provides sd files (single conformer, tautomers or multiple conformers). maintained by the institut de pharmacologie moléculaire et cellulaire, france. glass . glass (gpcr-ligand association) database is a manually curated repository for experimentally-validated gpcr-ligand interactions. along with relevant gpcr and chemical information, gpcr-ligand association data are extracted and integrated into glass from literature and public databases. a list of currently-known gpcrs was compiled from uniprot and used to filter through the other chemical databases for ligand-association data (chembl, bindingdb, iuphar, drugbank, pdsp), gpcr diseases association (ttd), gpcr experimental structural data (pdb, biolip), and predicted models of gpcrs (gpcrrd). subsequently, information from the extracted databases were unified to the same format and checked to ensure that all entries are only gpcr-related. thus, the user would not find any entries on receptor tyrosine kinases or any other protein that is not a gpcr. all relevant ligand chemical data (pubchem) and gpcr data (uniprot) were extracted accordingly for each gpcr-ligand entry. each molecule with a unique inchi key was considered a unique ligand entry in the database. developed and maintained by the zhang lab at the university of michigan, usa. chemdb/chemicalsearch . find chemicals by various search criteria. structural database (csd) . repository for small molecule crystal structures in cif format. the csd is compiled and maintained by the cambridge crystallographic data centre spresi web . integrated database containing over 8.7 million molecules, 4.1 million reactions, 658,000 references and 164,000 patents covering the years 1974 - 2009. developed by infochem. mmsinc . database of non-redundant, annotated and biomedically relevant chemical structures. includes

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