Chemical Informatics Letters

Volume 12, Issue 2; February 2006

Editor: Jonathan M Goodman

800 billion bases at the Sanger Institute
In January the Wellcome Trust Sanger Institute database of DNA sequences reached one billion entries. At 22 TB it is one of the biggest scientific RDBMS databases in the world.

The European ligand bank: a database of ligands for catalytic reactions in synthetic organic chemistry. Applications for membership are now invited.

Chemical Thesaurus
An index of chemical entities, from meta-synthesis, with about six thousand entries.

OpenDOAR - Directory of Open Access Repositories
This directory of open access repositories became available in January (Press release: PDF) currently contains 353 entries, all of which have been checked. Over a hundred chemistry resources are listed.

WWW statistics
This December survey of a billion web pages provides statistics on the types and styles of mark-up currently favoured. Most web pages have less than a hundred HTML tags, and, most commonly, use nineteen different sorts.

IUPAC provisional recommendations
IUPAC has made provisional recommendations for Quantities, Units and Symbols in _Physical Chemistry, a Glossary of Terms Relating to Pesticides and Explanatory Dictionary of Key Terms in Toxicology. The abstracts and full texts are available

Search Engines
New search engines since Chem. Inf. Letters 2004, 8, 7 include Amazon's a9, which finds places and gives pictures of the streets. For example, a search for 'Lensfield Road' produces a picture of the Cambridge Chemistry Department, which is on Lensfield Road, several pictures of the road and other buildings on it, and a few chemical schemes, which were published in papers from a Lensfield Road address. Microsoft's search engine, MSN search, has been updated. Yahoo has developed Y!Q, which analyses the web page you are reading and gives you related pages. AskJeeves has also been updated and no longer has a butler icon. Google still seems to lead the field, but competitors are also doing well. Companies which try to raise sites profiles on search engines seem to be doing good business, suggesting that search results can be manipulated. Ideas for search engine optimisation are available. A survey from SearchEngineWatch suggests that whilst search engines are sophisticated and intelligent, their users are not.

ACS electronic reprint policy
ACS Publications has recently modified its electronic reprint policy. Authors may distribute fifty free electronic reprints for the first year after publication. After this time, there is no restriction on the number of reprints accessed through author directed links.

This Protein Information Management System is sponsored by the BBSRC.

Structure-Function Linkage Database [SFLD]
A database that links evolutionarily related sequences and structures from mechanistically diverse superfamilies of enzymes to their chemical reactions. It is developed at the Babbitt and Ferrin labs at UCSF.

pKa Data and Calculation
Many programs are available for the calculation of the pKa of molecules, usually based on the correlation of sigma constants of functional groups with pKa. Some free programs and databases are listed here:

Punch List of Best Practices for Electronic Resources
This document published by the Engineering Libraries Division of the American Society for Engineering Education provides guidelines for the development of on-line resources.

© 2006 J M Goodman, Cambridge
Cambridge Chemistry Home Page CIL Chemical Calculations Chemical Information Laboratory Goodman Research Group Webmaster: J M Goodman