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.

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 - format conversion
• Bioclipse - a visual platform for chemical and bio-informatics.

Freely Available Databases

• ZINC Database
• PubChem
• KEGG

Free information

• MMCC Results Newsletter
• Chemical Informatics @ Wikipedia]
• Computational Chemistry List

Free to Academics engaged in non-commercial projects, etc.

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

Feeware

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

Database Vendors

• MDL
• Beilstein

Applications

• Docking: virtual screening

- DOCK - FRED - ICM - Glide

• Docking: accurate geometries

- GOLD - FlexX

• De Novo Design

- One

• Database Management Systems

- Daylight - MDL -

• Desktop modeling

- PyMol - Chimera

• Comprehensive Packages
• 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