Category:Free: Difference between revisions

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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, 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 cheminformatics software =
The [http://www.blueobelisk.com Blue Obelisk Movement] collects free software and databases. We note some of these, as well as other packages, below:
* [http://jmol.sourceforge.net JMol]
* [http://cdk.sourceforge.net CDK] - many of these packages, such as Bioclipse, make use of CDK.
* [http://openbabel.sourceforge.net OpenBabel]/[http://joelib.sourceforge.net/ JOELib] - format conversion
* [http://www.bioclipse.net Bioclipse] - a visual platform for chemical and bio-informatics.
* [http://www.knime.org Knime] - a free Scitegic PipelinePilot style program
* [http://www.mayachemtools.org MayaChemTools] - a growing collection of Perl scripts, modules, and classes to support day-to-day computational discovery needs
* OpenBabel


= Free databases =
= Free databases =
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* [http://www.cheminformatics.org/datasets/li/bbp2.smi Blood-brain-barrier penetration set]
* [http://www.cheminformatics.org/datasets/li/bbp2.smi Blood-brain-barrier penetration set]
* [http://cheminfo.informatics.indiana.edu/cicc/cis/index.php/Main_Page Chemical Information Wiki]
* [http://cheminfo.informatics.indiana.edu/cicc/cis/index.php/Main_Page Chemical Information Wiki]
= Free cheminformatics software =
The [http://www.blueobelisk.com Blue Obelisk Movement] collects free software and databases. We note some of these, as well as other packages, below:
* [http://jmol.sourceforge.net JMol]
* [http://cdk.sourceforge.net CDK] - many of these packages, such as Bioclipse, make use of CDK.
* [http://openbabel.sourceforge.net OpenBabel]/[http://joelib.sourceforge.net/ JOELib] - format conversion
* [http://www.bioclipse.net Bioclipse] - a visual platform for chemical and bio-informatics.
* [http://www.knime.org Knime] - a free Scitegic PipelinePilot style program
* [http://www.mayachemtools.org 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 Drug Discovery =  

Revision as of 15:57, 18 March 2014

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

  • 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

Free cheminformatics software

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.

Subcategories

This category has the following 2 subcategories, out of 2 total.

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Pages in category "Free"

The following 17 pages are in this category, out of 17 total.