Category:Cheminformatics: Difference between revisions

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== Freeware ==
== Freeware ==
Most completely free software for chemical informatics is part of the [http://www.blueobelisk.com Blue Obelisk Movement]. We note some of these, as well as other packages, below:
[[:Category:Free | Free software]]
* [http://jmol.sourceforge.net JMol] - so good, Nature picked it.
* [http://cdk.sourceforge.net CDK] - many of these packages, such as Bioclipse, make use of CDK.
* [http://openbabel.sourceforge.net OpenBabel]/[http://joelib.sourceforge.net/ JOELib] - format conversion
* [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.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 ==  

Revision as of 16:42, 11 March 2014

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. Our contribution in this area includes SEA.


Blogs and Communities

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

Free software

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


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

Useful Sites

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


Journals

Subcategories

This category has the following 2 subcategories, out of 2 total.

R

S

  • SEA‎ (1 C, 8 P)
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