Cheminformatics
Below are some useful links to Cheminformatics and QSAR
pages
What is Cheminformatics? A nice introduction by Craig James
http://www.emolecules.com/doc/cheminformatics-101.htm
Search for chemicals on emolecules.com or Chemindustry.com
Install MDL's Chemistry Plugin
How you can configure your browser to view rotating 3D chemical structures.
InChi - IUPAC 's new format for Chemical structures
http://www.iupac.org/inchi/ and the unnoficial FAQ http://wwmm.ch.cam.ac.uk/inchifaq/index.html
An interesting paper on the WWW for chemistry
http://www.ch.ic.ac.uk/rzepa/obc/
Open Babel A program to convert between molecular formats
http://openbabel.sourceforge.net/wiki/Main_Page
JCAMP-DX spectral file formats and XML http://www.jcamp.org/
Rajarshi Guha's great page of Python scripts. Somewhere he had a script for extracting .mol files from .sdf files
A fantastic freeware SDF viewer, 'Chemfile Browser' is available from http://www.hyleos.net/ and an ActiveX .mol file viewer called 'ChemView'
Cheminformatics.org A really useful list maintained by Andreas Bender
Open Source software for Cheminformatics http://www.blueobelisk.org/
QSAR Sites
Below are links to a number of useful QSAR resourcesBiological activity:
New NCBI site for chemistry Pubchem
TOXNET - Databases on toxicology, hazardous chemicals, environmental health, and toxic releases
DSSTox The Distributed Structure-Searchable Toxicity Database Network
Dictionary of Natural Products from Chapman &Hall/CRC
CHEMnetBASE also from Chapman &Hall/CRC has a huge range of chemical databases to search.
University of North Carolina, Chapel Hill has a searchable database of CNS drug activity PDSP Ki Database (NIMH Psychoactive Drug Screening Program)
Improving the Y for QSAR - A talk I presented at the UK QSAR society meeting 12th October 2004
Wikipedia has some excellent information on medicinal chemistry - see for example http://en.wikipedia.org/wiki/Aspirin
LogP calculations:
Online AlogP calculator AlogP
US EPA calculation suite (includes KOW) EPA
PSA calculator PSA
Syracuse KOW demo
Molinspiration.com Small calculator for molecular paramters
Molecular Parameters:
VEGA an amazing OpenGL based molecular modelling program from Alessandro Pedretti & Giulio Vistoli which is free for non-commercial use VEGA
DRAGON from the University of Milan (alas no longer freeware)
Virtual Computational Chemistry Lab VCC
Amino Acid encoding EvolvingCode
Miscellaneous Chemistry Links:
Tom's free chemistry software - no longer maintained but a great list
Spectral databases on the Internet:
NMR http://www.nmrshiftdb.org/
Metabonomics:
Standardised Reporting Structures for Metabonomics SMRS
See also Nature Biotechnology 23, 833 - 838 (2005)
A nice introduction to the use of Chemometrics for Pattern recognition in NMR data by Tim Ebbels
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