Chemical Informatics Letters

Volume 3, Issue 2; August 2001

• News
• Web Sites
• Glossary
• Archive

News:

Cybernetic Cells

The Scientific American (August 2001) has an article on computer models of cells and metabolic pathways, by W. Wayt Gibbs. 'Supercomputer models of living cells are far from perfect, but they are shaking the foundations of biology'. There are a number of web sites on this subject, including:

• Computer Simulation of Metabolism (Purdue) (index of web sites)
• BioNome
• Library of Mathematical Models of Biological Systems
• Mathematical Models in Molecular and Cellular Biology
• Protein Function and Biochemical Pathways (PFBP) Project

BMS acquires DuPont Pharmaceuticals

Bristol-Myers Squibb Company has purchased the DuPont Pharmaceuticals Company, a wholly-owned subsidiary of DuPont, for $7.8 billion.

GNU compiler for Java

The GNU project has released a compiler for the Java programming language. Various resources are available.

CAFASP

The goal of CAFASP is to evaluate the performance of fully automatic structure prediction servers available to the community. In contrast to the normal CASP procedure, CAFASP will answer the question of how well servers do without any intervention of experts, ie how well any user can predict protein structure. This may aid users in choosing which programs they wish to use, and in evaluating the reliability of the programs when applied to their specific prediction targets. Mirrors include: http://cubic.bioc.columbia.edu/mirror/cafasp/

ClogP

Oft quoted - but what is it? Pomona college has an explanation. On-line calculation is also possible from the DayLight web site. the algorithm is copyright by the BioByte Corporation and Pomona College.

Cycorp

A supplier of 'fomalised common sense' using programs can extract meaning from web pages.

Fugue

A new sequence analysis tool from the Blundell Group in Cambridge.

MICE

The Molecular Interactive Collaborative Environment (MICE) project is developing new methods of collaborative, interactive visualization of complex scientific data. While most existing methods of representing scientific data are static and two-dimensional, the technologies being used and developed for MICE provide interactive, three-dimensional environments within which multiple users can examine complex datasets in real-time. J Mol Graph and Mol Mod 2001, 19, 280-287.

EMP

Enzymes and Metabolic Pathways database, EMP, is a unique and most comprehensive electronic source of biochemical data. It covers all aspects of enzymology and metabolism and represents the whole factual content of original journal publications.

Web Sites:

BRENDA

A collection of enzyme functional data available to the scientific community free of charge for academic, non-profit users.

ENZYME

Enzyme nomenclature site, based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB)

The Biotechnology Division: the National Institute of Standards and Technology

This is an index to databases of the thermodynamics of enzyme-catalyzed reactions, short tandem repeat DNA, and biological macromolecule crystallization.