Chemical Informatics Letters

Volume 14, Issue 6; June 2007

Editor: Jonathan M Goodman

c2k is continuing to provide up to date information about chemistry departments, learned societies and chemistry journals around the world. The last report was in June 2006 (Chem. Inf. Lett. 2006, 12, #6, 61). The database now lists 1935 departments from 142 countries. The United States of America has the most departments (636 - down one from last year), followed by France (101 - not all of which would be 'departments' by conventional UK nomenclature) and then Germany (89). Britain is hanging on in fourth place. There are now 3072 sites listed in total, including departments, learned societies and 860 chemistry-related journals. The automated checking process usually finds about twenty are inaccessible in a typical month. The database has slightly more entries than last year.

The DrugBank database is a bioinformatics and cheminformatics resource that combines drug data with drug target information. The database contains nearly over four thousand drug entries including more than a thousand FDA-approved small molecule drugs. It is a project of the Wishart research group at the University of Alberta.

Database of Protein-Ligand Binding Affinities
The Gilson Group, at the University of Maryland Biotechnology Institute, has developed a web-accesible database of binding affinities for biomolecules, modified biomolecules, and synthetic compounds. The database is described in Nucleic Acids Research 2007, 35, D198-D201 (doi:10.1093/nar/gkl999), and can be searched by compound or by target.

Patent peer review
The USPTO is experimenting with peer review for patents. This might help to prevent court cases on patent validity.

Scientific Commons
Scientific Commons aims to provide comprehensive and freely available access to scientific knowledge. The home-page suggests it currently links to over fifteen million publications. A search for chemistry suggests that this is currently an unrepresented field.

Nature Precedings
Nature Precedings (not 'proceedings') is a place for researchers to share pre-publication research, supplementary findings, and other scientific documents. Submissions are screened but do not undergo peer review. The chemistry section has seven entries currently, mainly focussing on chemical informatics and biological chemistry. The ChemWeb preprint server hosts many interesting articles, but is now closed to new submissions. The ACS refused to accept for publication anything which had previously appeared on the ChemWeb preprint server. Will the same thing happen with Nature?

How effective is the Hirsch-index?
The Hirsch index, h, is defined as the number of papers from a particular author or group with h or more citations. It is effective because it is robust to minor errors in databases, and straightforward to calculate (PDF;

ChemRank allows you to add papers to a database, make comments, and vote on how good it is. This should allow a community-wide ranking of papers. The site started at the end of May 2007, and has only a few papers so far.

Moodle is an open-source course management system, which helps create on-line learning communities. It has some information on Chemistry/Biochemistry.

Semantic Web: path ahead
The semantic web may make knowledge accessible to software agents, and despite many challenges ahead, it may become the way everybody works.

AutoDock 4
AutoDock, the molecular docking program, is now available under the GPL.

Elementeo is a chemical card game, created by a team of school children, aged about thirteen.

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