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. | 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. | ||
==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 == | == Freeware == | ||
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* [http://jmol.sourceforge.net JMol] - so good, Nature picked it. | * [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://cdk.sourceforge.net CDK] - many of these packages, such as Bioclipse, make use of CDK. | ||
* [http://openbabel.sourceforge.net OpenBabel] - format conversion | * [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.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 == | == Freely Available Databases == | ||
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[[Category:Chemical Informatics]] | [[Category:Chemical Informatics]] | ||
[[Category:Portal]] | |||
Revision as of 21:02, 20 September 2007
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.
Blogs and Communities
- Blue obelisk group
- Chemical blogspace – molecule aware feed aggregation
- CCL – Computational chemistry
- Docking – virtual screening and structure-based drug design
- eChemInfo
- Google group – Life science informatics
- Nature group – Life science informatics
- PostGenomics
- QSAR society
Data and directory services
Freeware
Most completely free software for chemical informatics is part of the Blue Obelisk Movement. We note some of these, as well as other packages, below:
- JMol - so good, Nature picked it.
- 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
Freely Available 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
Free information
- MMCC Results Newsletter
- Chemical Informatics @ Wikipedia]
- Computational Chemistry List
- Linux for Chemistry
- Caco-2 permeability
- Blood-brain-barrier penetration set
- Chemical Information Wiki
Free to Academics engaged in non-commercial projects, etc.
Useful Sites
- Rognan/Strasbourg
- Jain
Feeware
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