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
• KEGG - free to use online, and download via PubChem. For more access they request support.
• 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 websites

• Computational Chemistry List
• Linux for Chemistry
• Caco-2 permeability
• Blood-brain-barrier penetration set
• Chemical Information Wiki

Free cheminformatics software

• Rdkit
• Blue Obelisk - collection of free software and databases.
• JMol
• CDK - many of these packages, such as Bioclipse, make use of CDK.
• OpenBabel - format conversion and much more
• Bioclipse - a visual platform for chemical and bio-informatics.
• Knime - a free Scitegic PipelinePilot style program
• MayaChemTools - tools to support computational discovery needs

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.

• 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