Chemical informatics: Difference between revisions
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* [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 | * [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 | |||
== Freely Available Databases == | == Freely Available Databases == | ||
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* [http://bioinformatics.charite.de/superligands/ SuperLigands] - a PDB ligand database | * [http://bioinformatics.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 | |||
== Free information == | == Free information == | ||
Revision as of 00:10, 5 November 2011
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
- 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 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
- MayaChemTools - a growing collection of Perl scripts, modules, and classes to support day-to-day computational discovery needs
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
- ChemBlast - a tool to find the same ligand in many PDB structures
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
- smi23d - 3D Coordinate Generation
- Online SMILES Translator and Structure File Generator
- Molecule file conversion with MolConverter
- Search the CCL for others
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