Chemical informatics

From DISI

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.

1 Blogs and Communities
2 Data and directory services
3 Freeware
4 Freely Available Databases
5 Free information
6 Free to Academics engaged in non-commercial projects, etc.
7 Useful Sites
8 Feeware
9 Database Vendors
10 Applications
11 Docking Programs
12 US Government Grants
13 Journals

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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

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Data and directory services

Cheminformatics

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

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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

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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

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