Chemical informatics: Difference between revisions

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Chemical Informatics is the art and science of manipulating chemical structure, particularly in a biological context. Many but not all of us are mainly looking for new ligands for biological targets.
#REDIRECT [[Category:Cheminformatics]]
 
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==Blogs and Communities ==
* [http://blueobelisk.sourceforge.net Blue obelisk group]
* [http://cb.openmolecules.net/ Chemical blogspace] – molecule aware feed aggregation
* [http://ccl.net/ CCL – Computational chemistry]
* [http://docking.org/ Docking] – virtual screening and structure-based drug design
* [http://echeminfo.com/ eChemInfo]
* [http://groups.google.be/group/LifeScienceInformatics Google group – Life science informatics]
* [http://network.nature.com/group/lifescienceinformatics Nature group – Life science informatics]
* [http://www.postgenomic.com/ PostGenomics]
* [http://www.qsar.org QSAR society]
 
== Data and directory services ==
* [http://cheminformatics.org/ Cheminformatics]
 
* [http://redpoll.pharmacy.alberta.ca/drugbank/ DrugBank] The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains nearly 4300 drug entries including >1,000 FDA-approved small molecule drugs, 113 FDA-approved biotech (protein/peptide) drugs, 62 nutraceuticals and >3,000 experimental drugs. Additionally, more than 6,000 protein (i.e. drug target) sequences are linked to these drug entries. Each DrugCard entry contains more than 80 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data. Please cite: Wishart DS et al., DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 2006 1;34
 
== Freeware ==
Most completely free software for chemical informatics is part of the [http://www.blueobelisk.com Blue Obelisk Movement]. We note some of these, as well as other packages, below:
* [http://jmol.sourceforge.net JMol] - so good, Nature picked it.
* [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
 
== Freely Available Databases ==
* [[ZINC Database]]
* [[PubChem]]
** [http://www.ncbi.nlm.nih.gov/Class/PubChem/course.html Principles of PubChem NCBI Training Course]
** [http://www.indiana.edu/~cheminfo/PubChemHandout.doc PubChem Handout Word document (Dana Roth, Caltech) ]
 
* [[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/superligands/ SuperLigands] - a PDB ligand database
* [http://cheminf.cmbi.ru.nl/biometa/ BioMeta ] - a database of metabolites derived from KEGG
 
== Free information ==
* [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://www.redbrick.dcu.ie/~noel/linux4chemistry/ Linux for Chemistry]
* [http://pubs3.acs.org/acs/journals/supporting_information.page?in_manuscript=ci049884m Caco-2 permeability]
* [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]
 
 
 
== Free to Academics engaged in non-commercial projects, etc. ==
* [http://www.chemaxon.com ChemAxon JChem Marvin]
* [http://www.eyesopen.com OpenEye]
* [http://www.xemistry.com Cactvs]
* [http://www.cgl.ucsf.edu Chimera]
* [http://pymol.sourceforge.net PyMol]
*
 
== Useful Sites ==
* [http://bioinfo-pharma.u-strasbg.fr/template/jd/index.php Rognan/Strasbourg]
* Jain
* [http://www.chembiogrid.org/cheminfo/smi23d/ smi23d - 3D Coordinate Generation]
* [http://cactus.nci.nih.gov/services/translate/ Online SMILES Translator and Structure File Generator]
* [http://www.chemaxon.com/marvin/doc/user/molconvert.html Molecule file conversion with MolConverter]
* [http://www.ccl.net/ Search the CCL for others]
 
== Feeware ==
* [http://www.molecularnetworks.com Molecular Networks]
* [http://www.molinspiration.com Molinspiration]
* [http://www.schrodinger.com Schrodinger]
* [http://www.pipelinepilot.com Pipeline Pilot]
* [http://www.biosolveit.com BioSolveIT]
* [http://www.daylight.com Daylight]
 
 
== Database Vendors ==
* MDL
* Beilstein
*
 
 
== Applications ==
 
== Docking Programs ==
There is a dedicated page for [[Available Docking Programs]].
=== De Novo Design ===
- One
 
=== Database Management Systems ===
- Daylight
- MDL
- Oracle
- MySQL
 
=== Desktop modeling ===
- PyMol
- Chimera
* Comprehensive Packages ( Accelrys, Sybyl, etc)
* ADME(T)
* QSAR
* Bioisosteres
* hit-to-lead
 
== US Government Grants ==
* P20 ECCR
* NIH Roadmap
 
 
== Journals ==
* [http://pubs3.acs.org/acs/journals/toc.page?incoden=jcisd8 JCIM]
* [http://springerlink.metapress.com/content/1573-4951/ JCAMD]
* [http://pubs3.acs.org/acs/journals/toc.page?incoden=jmcmar J Med Chem]
* [http://pubs3.acs.org/acs/journals/toc.page?incoden=jacsat JACS]
* [http://www.pnas.org/ PNAS]
* [http://www.chemistrycentral.com/ CCJ Chemistry Central Journal]
* [http://www.biomedcentral.com/ BioMed Central]
* [http://www.biomedcentral.com/browse/bysubject/  Curr. Op. Drug Discov. Devel.]
* [http://www.elsevier.com/locate/issn/13675931 Curr. Op. Chem. Biol.]
* [http://www.nature.com/nature/ Nature]
* [http://www.sciencemag.com/ Science]
* [http://www.nature.com/nbt/ Nature Biotech.]
* [http://www.nature.com/drugdisc/ Nature Drug Discov.]
* [http://www.nature.com/nchembio/ Nature Chem. Biol.]
 
 
[[Category:Chemical Informatics]]
[[Category:Portal]]

Latest revision as of 23:35, 24 February 2014

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