The modern world has brought us nuanced ideas about what free means. Fortunately, many, many resources for drug discovery are free to use (gratis) for academics, as long as you abide by the rules. A growing number of resources are even freer (libre). You must read the license to know which one you've got.

Free databases, programs and services referenced on this site are tagged as free to make them easy to find here. Some things are only free to academics, some only for qualifying academic projects. We called these Category:Freecom meaning a free/commercial mixed model. Here we collect things that are generally freely available (gratis) at least to academics. Please also see Category:Commercial.

Free databases

• ZINC Database, DUDE, Aggregator Advisor
• 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

Free cheminformatics software

• Rdkit

The Blue Obelisk Movement collects free software and databases. We note some of these, as well as other packages, below:

• JMol
• 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
• OpenBabel

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