Free databases, programs and services are tagged as free to make them easy to find here. Some things are only free to academics, or qualified academics. We called these Category:Freecom meaning free/commercial mixed model. Others require a contract, but cost no money. You must read the fine print. Here we collect things that are generally freely available at least to academics. Please also see Category:Commercial and Category:Freecom. Distinguish between free to use (gratis) vs free to develop (libre).

Free cheminformatics software

Most completely free software for chemical informatics is part of the Blue Obelisk Movement. We note some of these, as well as other packages, below:

• JMol - so good, Nature picked it.
• CDK - many of these packages, such as Bioclipse, make use of CDK.
• OpenBabel/JOELib - format conversion
• Bioclipse - a visual platform for chemical and bio-informatics.
• Knime - a free Scitegic PipelinePilot style program
• MayaChemTools - a growing collection of Perl scripts, modules, and classes to support day-to-day computational discovery needs

Free databases

• ZINC Database
• PubChem
  • Principles of PubChem NCBI Training Course
  • PubChem Handout Word document (Dana Roth, Caltech)

• KEGG
• ChemDB @ UCI - public database of small molecules and related chemical informatics resources
• SuperDrug - a conformational drug database
• SuperNatural - searchable database of available natural compounds
• SuperLigands - a PDB ligand database
• BioMeta - a database of metabolites derived from KEGG
• ChemBlast - a tool to find the same ligand in many PDB structures

Free datasets

• MMCC Results Newsletter
• Chemical Informatics @ Wikipedia]
• Computational Chemistry List
• Linux for Chemistry
• Caco-2 permeability
• Blood-brain-barrier penetration set
• Chemical Information Wiki

Open Source Drug Discovery

Open Source is well known in the computer science community, and indeed in bioinformatics. A number of initiatives that include small molecule drug design have been launched. They are attempting to discover 'open source drugs', however strange that may sound. We ignore here initiatives that aim to develop vaccines, not because they are not important, but because our interest is in small molecules.

• BioForge : A community for biological innovation
  • BIOS : Biological Innovation for Open Society
  • Patent Lens Global resource for increasing patent transparency
• TDI : tropical disease initiative
  • TSL : The Synaptic Leap
• MMV : Medicines for Malaria Venture
• DNDi : Drugs for Neglected Diseases initiative
• TBA : TB Alliance
• OWH : One World Health