Volume 6, Issue 5; May 2003
Editor: Jonathan M Goodman
- BioSimGrid is a Grid database for biomolecular simulations, run by collaborators in Oxford, Southampton, London, Birmingham, Nottingham and York, lead by Professor Mark Sansom at Oxford's biochemistry department. The project aims to develop a 'kite-mark' (quality standard) for biomolecular simulations and suitable metadata, in addition to a distributed database.
Chemical Resource Kit [CRK]
- The (CRK intends to offer a graphical interface to archive, data entry and presentation of chemical information, as well as useful tools for data modelling. It will also a modern ab initio computational process for calculating chemical structures and properties, and a browser-based access pathway. It has been developed by Alex Clark, until recently a post doc with Professor Chris Reed at UC Riverside, and now at Intellichem.
- GRID computing: What a developer needs to know to get started is a short overview from IBM developerWorks. How does Grid compare to P2P? Both are ways of sharing computer power. A paper submitted to the 2nd International Workshop on Peer-to-Peer Systems provides an answer (PDF file). CERN has announced the CERN openlab for DataGrid applications a collaboration between CERN and industrial partners to develop data-intensive Grid technologies to be used by the worldwide community of scientists working at the next-generation Large Hadron Collider. It will handle petabytes of information every year.
AMBER parameter database
- This database keeps track of new parameters developed for the AMBER forcefield. It is maintained by Richard Bryce at Manchester University's Department of Pharmacy.
Enhanced stereochemistry from MDL
- The description of the stereochemistry of a molecule is a difficult problem, and it is hard to convey the difference between relative and absolute stereochemistry of different centres within a single structure. MDL has developed a method to deal with this problem (Full paper).
Protein Informatics Group
- This group at the Oak Ridge National Laboratory in Tennessee develops computational tools for solving problems from molecular biology.
- The Society of Environmental Toxicology and Chemistry promotes multidisciplinary approaches to solving environmental problems. It was founded in 1979 to balance the interests of academia, business, and government, and has over 5000 members in over seventy coutries, and publishes several journals.
- The goal of this database is to facilitate access to www resources for researchers working in the field of P450 proteins and P450-containing systems. It is run from the International Centre For Genetic Engineering And Biotechnology in Italy.
DOD Computational Chemistry and Materials Science [CCM]
- The The USA Department of Defence High Performance Computing Modernization Program includes chemical projects. Current projects include: Toxicological assessment of FDA-approved treatments for acute organophosphate exposure; Mechanism of action for qinghaosu-based antimalarial drugs; Cyanide prophylaxis.
- The American Mathemetical Society's mathematical reviews on the web, including condensed matter physics, informatics, and computer modelling.
- This institute offers training in Cheminformatics. The website is not clear about the academic credentials of the institute.
Professor John C Huffman
- Professor John Huffman is director of the Indiana University Molecular Structure Center (IUMSC) and a professor of informatics at Indiana University's School of informatics. The IUMSC is the hub of Reciprocalnet, a distributed database used by research crystallographers from fourteen institutions to store information about molecular structures.
© 2003 J M Goodman, Cambridge