Category:Free: Difference between revisions

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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 ([http://en.wikipedia.org/wiki/Gratis_versus_libre libre]). You must read the license to know which one you've got.
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 ([http://en.wikipedia.org/wiki/Gratis_versus_libre libre]). You must read the license to know which one you've got.
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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 =
* [[ZINC Database]]
* [[ZINC Database]], [[DUDE]], [[Aggregator Advisor]]
* [[PubChem]]
* [[PubChem]]
** [http://www.ncbi.nlm.nih.gov/Class/PubChem/course.html Principles of PubChem NCBI Training Course]
* [[KEGG]] - free to use online, and download via PubChem. For more access they request support.
** [http://www.indiana.edu/~cheminfo/PubChemHandout.doc PubChem Handout Word document (Dana Roth, Caltech) ]
* [http://bioinf-applied.charite.de/supernatural_new/index.php SuperDrug] - a conformational drug database
 
* [[KEGG]]
* [http://cdb.ics.uci.edu/CHEM/Web/ ChemDB @ UCI] - public database of small molecules and related chemical informatics resources
* [http://bioinf.charite.de/superdrug/ SuperDrug] - a conformational drug database
* [http://bioinformatics.charite.de/supernatural/ SuperNatural] - searchable database of available natural compounds
* [http://bioinformatics.charite.de/supernatural/ SuperNatural] - searchable database of available natural compounds
* [http://bioinformatics.charite.de/superligands/ SuperLigands] - a PDB ligand database
* [http://bioinf-tomcat.charite.de/superligands/ SuperLigands] - a PDB ligand database
* [http://cheminf.cmbi.ru.nl/biometa/ BioMeta ] - a database of metabolites derived from KEGG
* [http://cheminf.cmbi.ru.nl/biometa/ BioMeta ] - a database of metabolites derived from KEGG
* [http://xpdb.nist.gov/chemblast/pdb.pl ChemBlast] - a tool to find the same ligand in many PDB structures
* [http://xpdb.nist.gov/chemblast/pdb.pl ChemBlast] - a tool to find the same ligand in many PDB structures


= Free datasets =
= Free websites =
* [http://ccl.net/cca/documents/MMCC_Results/ MMCC Results Newsletter]
* [http://en.wikipedia.org/wiki/Computational_chemistry Chemical Informatics @ Wikipedia]]
* [http://ccl.net Computational Chemistry List]
* [http://ccl.net Computational Chemistry List]
* [http://www.redbrick.dcu.ie/~noel/linux4chemistry/ Linux for Chemistry]
* [http://www.redbrick.dcu.ie/~noel/linux4chemistry/ Linux for Chemistry]
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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 =
* [[Rdkit]]
* [http://sourceforge.net/projects/blueobelisk/ Blue Obelisk]  - collection of free software and databases.
* [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] -  format conversion and much more
* [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] - tools to support computational discovery needs


= Open Source Drug Discovery =  
= 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.
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.
* [http://bioforge.net BioForge] : A community for biological innovation
 
** [http://www.bios.net BIOS : Biological Innovation for Open Society]
* [http://www.patentlens.net Patent Lens ] Global resource for increasing patent transparency
** [http://www.patentlens.net Patent Lens ] Global resource for increasing patent transparency
* [http://www.tropicaldisease.org TDI : tropical disease initiative]
* [http://www.tropicaldisease.org TDI : tropical disease initiative]
** [http://www.thesynapticleap.org TSL : The Synaptic Leap]
* [http://www.thesynapticleap.org TSL : The Synaptic Leap]
* [http://www.mmv.org MMV : Medicines for Malaria Venture]
* [http://www.mmv.org MMV : Medicines for Malaria Venture]
* [http://www.dndi.org DNDi : Drugs for Neglected Diseases initiative]
* [http://www.dndi.org DNDi : Drugs for Neglected Diseases initiative]
* [http://www.tballiance.org TBA : TB Alliance]
* [http://www.tballiance.org TBA : TB Alliance]
* [http://www.oneworldhealth.org OWH : One World Health]


[[Category:Portal]]
[[Category:Attributes]]
[[Category:Attributes]]

Latest revision as of 04:43, 3 June 2015

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

Free websites

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.

Subcategories

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

Z

Pages in category "Free"

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

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