Chemical informatics

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

• Cheminformatics

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

• ZINC Database
• PubChem
  • Principles of PubChem NCBI Training Course
  • PubChem Handout Word document (Dana Roth, Caltech)

• 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.

• ChemAxon JChem Marvin
• OpenEye
• Cactvs
• Chimera
• PyMol

Useful Sites

• Rognan/Strasbourg
• Jain

Feeware

• Molecular Networks
• Molinspiration
• Schrodinger
• Pipeline Pilot
• BioSolveIT
• Daylight

Database Vendors

• MDL
• Beilstein

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

• JCIM
• JCAMD
• J Med Chem
• JACS
• PNAS
• CCJ Chemistry Central Journal
• BioMed Central
• Curr. Op. Drug Discov. Devel.
• Curr. Op. Chem. Biol.
• Nature
• Science
• Nature Biotech.
• Nature Drug Discov.
• Nature Chem. Biol.