Chemical Informatics Letters

Volume 10, Issue 2; February 2005

Editor: Jonathan M Goodman

Syracuse Research Corporation
The Syracuse Research Corporation provides a variety of free services including a PBT Profiler for estimating Persistent, Bioaccumulative, and Toxic Profiles of organic chemicals, Estimation software which calculates a variety of properties and is available from Environmental Protection Agency and a database of Environmental Fates. Other resources are also available for purchase, including a Physical Properties Database and its free demo version.

Virtual Screening and Structure-Based Drug Design
The CHI conferences: a conference on Virtual Screening will run March 30th-31st in Boston and another conference Structure-Based Drug Design will take place from May 24th-26th in Philadelphia. Highlights include lectures from Professor Richard A Friesner and by Dr Matthew Stahl.

IBM Opens Their Patent Portfolio to Open Source
IBM has undertaken not to assert five hundred of their forty thousand software patents against Open Source Software in support of innovation and open standards (Announcement (PDF file) and Press release). Sun also announced that it will provide access to sixteen hundred patents for the open source community. Richard Stallman comments that this is a good thing, but does not remove the need to fight against the software patent system. Linus Torvalds notes that software patents are a problem, despite these announcements. The European Parliament has just decided not to pass a bill which would have allowed software patents.

Internet Journal of Chemistry
The Internet Journal of Chemisty is to stop publication. It was launched in January 1998 and provided innovative web-based services. The existing journal articles will continue to be available for free for the foreseeable future.

Why don't chemists like preprints?
Is the chemical community not interested in this form of publication? There is some evidence, in computer science, that open access papers are cited more, and astrophysics papers published as pre-prints are also cited more. Why not chemistry?


(i) Refereeing services: So chemists rely more on referees than other disciplines? Checking experimental data is laborious. Perhaps some subjects rely less on this, particularly if they may often publish ideas without data or analyses of shared data?
(ii) Tradition: in some respects the process of publishing new syntheses has been similar for over a century. Is it inertia that discourages preprints and open access publication?
(iii) Power of established publishers: need good names as editors and track record. There are big players who are hard to challenge. Chemistry was good business in nineteenth century; maths and biology were not.

Grand Challenges in Computing
The British Computer Society is running a conference considering the grand challenges in computing. These include complete simulations of living organisms, global and scalable ubiquitous computing, managing information over a lifetime, the architecture of the brain, and non-classical computing.

Search Engines
Search engines were last mentioned here in Chem. Inf. Letters 2004, 8, 7. New search engines include Amazon's a9, which finds places and gives pictures of the streets. For example, a search for 'Havemeyer Hall' produces a picture of the Columbia University Chemistry Department. Microsoft has a new search engine: MSN search. Yahoo has developed Y!Q, which analyses the web page you are reading and gives you related pages. Google still seems to lead the field, but competitors are doing a an increasingly good job. Companies which try to raise sites profiles on search engines seem to be doing good business, suggesting that the results can be manipulated. A survey from SearchEngineWatch suggests that whilst search engines are sophisticated and intelligent, their users are not.

Open health standards
Some of the largest US technology companies have agreed to embrace open, nonproprietary technology standards as the software building blocks for a health information network in the USA.

Maintaining Chemical Information
Two historians who have questioned how industry reacts when faced with information about potential dangers from their products are being sued, as are the book's referees. Good chemical information can save lives.

NIH Calls on Scientists to Speed Public Release of Research Publications
The NIH has announced a new policy - it calls on scientists to release the public manuscripts from NIH-supported research within twelve months of publication (PDF). PubMedCentral (PMC), a free digital archive run by the NIH, provides the resources needed to do this. More information is available from the NIH website. The Nature Publishing Group (NPG) has changed its policy to Allow authors to publish articles on an archive. Authors will be encouraged to submit the manuscript to their funding body's archive, their institution's repositories and their personal websites six months after publication. The Nature license is available (PDF).

Molecular Descriptors Calculation
preADME is a web-based program which calculates molecular descriptors which can be used to estimate ADME properties. It was developed at the Research Institute of Bioinformatics and Molecular Design in Korea. The Dragon 5 program, from the Todeschini Group in Milan, calculates 1661 molecular descriptors, but is not freely available to download, but an online version is available from the Virtual Computational Chemistry Laboratory.

Drug names
The World Health Organization has a web site which lists information about some drug names, and also sells a CD-ROM with more information. Fuller on-line list are also available from other sources.

© 2005 J M Goodman, Cambridge
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