Category:Cheminformatics

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, or trying to predict the function of proteins by the ligands they recognize. Our contribution in this area includes SEA, with ZINC in a supporting role.

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

• 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

Free cheminformatics software

Free software

Freely Available Databases

free databases

Free datasets

free datasets

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

Free or cheap to academics, costs to companies (freecom)

Useful Sites

Useful Websites

Feeware

Commercial software.

Database Vendors

Commercial database vendors.

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

Journals

Journals