Chemical Informatics Letters

Volume 14, Issue 2; February 2007

Editor: Jonathan M Goodman

The end of open review in Nature
The editors of Nature have ended their experiment in open review, which allowed authors who passed an initial editorial assessment to post their papers on-line for open and signed reviews. About five per cent of authors chose this option, but the comments on the papers had less detailed analysis than would be expected from a referee, and many papers received no comments. PlosOne publishes papers using a somewhat similar scheme, and is continuing to do so.

Galapagos acquires Inpharmatica
Inpharmatica, which uses informatics in medicinal chemistry and ADME to help drug discovery, has been acquired by Galapagos, a genomics-based drug discovery company. BioFocusDPI has also been acquired.

UK Government closes websites to improve information transfer
The UK government has run almost a thousand websites, mainly in the domain. More than five hundred will now be closed, and only twenty six will definitely remain.

e-Therapeutics is a systems biology drug discovery company, whose CEO is Professor Malcolm Young from Newcastle University.

CSA trust newsletter
The Winter Newsletter of the Chemical Structure Association Trust is now available.

Front page to the internet
Google is now so powerful that it might be considered to be the internet's front page. If a site is not listed on Google, does it become invisible?

Search Engines
Changes in search engines since Chem. Inf. Letters 2006, 12, 19 include a list of a hundred new search engines. The website SearchEngineWatch continues to monitor developments. The Wiki Search project is aiming to revolutionise searching in a Wikipedia-inspired way.

Synthesis Design
How good are computers at designing syntheses for molecules? A number of programs have been described recently: ARChem - Route Designer (Automating Retrosynthetic Chemistry) is an expert system from SimBioSys which helps chemists design synthetic routes. SimSoup is a graphical Artificial Chemistry simulator, which calculates how groups of molecules interact. ROBIA is a reaction prediction program.

A software environment for statistical analysis, molecular viewing, descriptor generation, and similarity search. The last update was released in March 2005, from the National Institute of Statistical Sciences.

Chemical structure look-up service
The chemical structure look-up service (CSLS ) was developed at the NCI CADD Group headed by Dr. Marc Nicklaus. It searches over eighty databases and over twenty seven million structures.

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

XDrawChem is a two-dimensional molecule drawing program for Unix operating systems, last updated in 2005.

© 2007 J M Goodman, Cambridge; Chemical Informatics Letters ISSN 1752-0010
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