This website contains links to cheminformatics programs and QSAR datasets (with structures!). All programs should be free to use, at least for academics. For a computational chemistry mailing list, see, the QSAR society with additional resources can be found at has been featured in Current Opinion in Drug Discovery and Development! (2004 7(4), 393-394; 2005 8(3) 294-295).

Cheminformatics Links
635 Links in 90 Categories Online!
  • Added 35 links (20 Aug 2005)
    • Human Protein Reference Database - Proteins, interactions and disease associations for >18,000 proteins with >27,000 interactions
    • DrugBank - More than 4,000 experimental/approved drugs linked to > 15,000 target proteins
    • CHMIS-C - Comprehensive Herbal Medicine Information System for Cancer Drug Design; > 500 recipies, >900 ingredients, >9,000 associated small molecules
    • PerlMol - A collection of Perl modules for cheminformatics and computational chemistry
    (Click the "What's new" button in the link directory to locate these and other new entries or use the search option).

  • Added ~ 50 links (now 600!): (2 May 2005), e.g.
    KiBank Ki database, Agent2 and Quacpac tautomer enumeration, PowerMV molecular data analysis environment, Molecular Diversity Preservation Database, Online Similarity Search tools, Compumine Rule Discovery System, ChemMine chemical genomics database, MINT Molecular Interactions Database, INChI Generator, eHiTs Docking program, ...
[complete list of updates]
Data Sets
(QSAR, QSPR, BBB penetration, Caco2 permeability, ...)
44 Datasets in 9 Categories Online!
20 Aug 2005: 3 New Datasets
  • Li Blood-Brain-Barrier Penetration Dataset (415 compounds with binary classification plus references)
  • Fontaine Factor Xa Dataset (335 compounds with Factor Xa inhibition data)
  • Karthikeyan Melting Point Dataset (4173 compounds with melting points from 14-392.5 degrees Celsius)
  • Jorissen/Gilson 5 Classes Dataset (50 Compounds against 5 activity classes each, plus Decoys) (12 June 2005)
  • Guha PDGFR Inhibitor dataset (79 compounds with inhibition data) (12 June 2005)
  • Guha Artemisinin Inhibitors dataset (179 compounds with antimalarial activity relative to Artemisinin) (2 May 2005)
  • Amicbase Toxicity Dataset (300 compounds with LD50 data) (2 May 2005)
  • Carcinogenicity Dataset (774 compounds with TD50 data) (2 May 2005)
  • Bursi AMES Toxicity Dataset (4337 Compounds) (25 March 2005)
[complete list of updates]
Molecular Similarity Search
Online comparison of query to library (max. ~1000 structures). Uses circular fingerprints (see references) and the Tanimoto coefficient.
MOLPRINT 2D now also downloadable for local installation
Online Diversity Assessment
Online diversity assessment of chemical libraries. Diversity is compared relative to an "ideal diverse" library.
  Review on Molecular Similarity,
written for Organic and Biomolecular Chemistry
- see this website for the PDF! (For copyright reasons not on this site.)

Molecular Similarity Methods
CPGS thesis, including molecular similarity review

This non-commercial web site compiles information on cheminformatics web resources. Please contact me if you would like to include information. Andreas Bender - e-mail: andreasb [] - ICQ 166 835 816