Chemical informatics: Difference between revisions

From DISI
Jump to navigation Jump to search
No edit summary
 
(Redirected page to Category:Cheminformatics)
 
(10 intermediate revisions by 2 users not shown)
Line 1: Line 1:
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]]
 
 
==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]
 
== 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
 
== 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

Redirect to:

Retrieved from "http://wiki.docking.org/index.php?title=Chemical_informatics&oldid=6285"