Chemical Informatics Letters

Volume 9, Issue 6; December 2004

Editor: Jonathan M Goodman

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Survey of molecular modelling programs

Last reviewed in Chemical Informatics Letters 2003, 7, #6. This list excludes the major commercial molecular modelling packages and concentrates on programs for which the source code is available in some form and which are available freely or cheaply. Usually there is a license agreement restricting what may be done with the source code.

AMBER: Originally developed by Peter Kollman, and now maintained by Professor David Case' group at the Scripps Research Institute and collaborators, AMBER 8 costs $400 for an academic license, which includes source code.
AMMP: A molecular mechanics and dynamics program written in C by Professor Robert Harrison at Georgia State's Computer Science Department. It is some time since the program was last updated.
B: B, formerly Biomer; Free; Source Code; Java. Has moved from its old location to Professor David Case' group at the Scripps Research Institute. The page was last updated on 11th October 2002.
CPMD: A plane wave/pseudopotential implementation of Density Functional Theory. The CPMD group is coordinated by Professor Michele Parrinello (Director of the Swiss Center of Scientific Computations and Professor at the ETH Zuerich) and Dr Wanda Andreoni (Manager of the Computational Material Science Group at IBM Zurich Research Laboratory). An e-mail discussion list is available to discuss the program. Last updated May 2004.
DALTON: A quantum chemistry program using SCF, MP2, MCSCF or CC wave functions. The strengths of the program are mainly in the areas of magnetic and (frequency-dependent) electric properties, and for studies of molecular potential energy surfaces. The main authors are T. Helgaker, H. J. A. Jensen, P. Jorgensen, J. Olsen, K. Ruud, H. Ågren. DALTON 2.0 is expected at the end of 2004.
FSatom: Free software project for atom scale simulation, which will incorporate Molecular Dynamics and Force Fields, Quantum Chemistry and Density Functional Methods. It is not clear if this program has been updated in 2004; the mailing list has not been active since February.
GAMESS-UK: Ab initio calculations. A software company, Computing for Science, now administers GAMESS-UK, which remains free to UK academics. Martyn Guest, of the Daresbury Laboratory, is the main author. Version 6.3 is now available.
GAMESS-US: Ab initio calculations. The program is maintained by Dr Mark Gordon's research group at the Ames Laboratory. Last updated November 2004.
Ghemical: A computational chemistry software package released under the GNU GPL; C++; Linux. Developed in Finland by Tommi Hassinen and collaborators. Last updated December 2002.
GROMACS: A molecular dynamics package, available under GPL, initially developed by Herman Berendsen at Groningen University. Last modified March 2004 (version 3.2.1).
GULP: A molecular modelling program for periodic solids, gas phase cluseters and isolated defects, written by Julian Gale. Last updated June 2004.
InterChem: This program provides an interface to other programs and is free to academics; Last updated June 2001.
MMTK: Open Source Project; Mainly written in Python,with a small amount of C; Konrad Hinsen, from CNRS Orleans, who is also involved with FSatom (vide supra). There is now a MMTK Wiki, which has been updated this month. MMTK was updated in 2004.
nMOLDYN: An analysis program for molecular dynamics simulations, which interacts with MMTK. There is a nMOLDYN Wiki. The current version is 2.2.1.
MOLPRO: A quantum chemistry package developed by Professor Peter Knowles at Cardiff University and Professor Hans-Joachim Werner at Stuttgart University.
NWChem: A computational chemistry package that is designed both for workstations and high-performance parallel supercomputers, developed in the William R Wiley Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory, USA. Version 4.6 available in May 2004.
Tinker: A free, full source code (Fortran) molecular mechanics and dynamics program, written in the Ponder Lab. Last updated in June 2004.
YUP: Yammp under Python. There are several methods for energy minimisation, molecular dynamics and Monte Carlo. From the Harvey Lab at the Georgia Institute of Technology. Last updated October 2004.

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BIOS

The Biological Innovation for Open Society (BIOS) initiative aims to make the latest genetics and biology tools freely available to researchers over the internet. BIOS encourages companies to contribute their research tools and technologies to the BioForgerepository. In return, users of the technology are bound by an open source license to share all improvements. This is an intiative of CAMBIA, the Center for the Application oof Molecular Biology to International Agriculture.

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GUI design

What is the best way to design a graphical user interface? This article provides a series of useful guidelines, including an emphasis on getting the user's work done rather than encouraging them to appreciate the interface.

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Chemophilia

'The environmental chemistry web site for balanced comment on media reports which feed public concern and the growth of chemophobia." This site has been running since 1998, from Chemical and Bioanalytical Sciences at Royal Holloway, University of London.

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World Community Grid

The World Community Grid's mission is to create the largest public computing grid benefiting humanity. Projects include a human proteome folding project. Partners include IBM and United Devices. Information on submitting proposals is available, and web-users are asked to join the grid (provided they are running Windows software).

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European PubMed?

The Wellcome Trust is interested in establishing a European archive, inspired by the US National Library of Medicine's PubMed Central which has NIH funding. In due course, it may be that all Wellcome Trust funded research will be placed in a public access archive within six months of publication. The Foundation for Information Policy Research has called for the establishment of a European refence library system to which all publishers would have to contribute an unprotected electronic copy of everything over which they wish to exercise powers of copyright, following the precedent of existing Legal Deposit Libraries in the UK and Ireland. BBC radio recently broadcast an analysis of open access publishing: Publish or Be Damned (listen to the programme).

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House of Commons Science and Technology Committee - Fourteenth Report

The UK's House of Commons science and technology committee has published a report on scientific publishing. This follows from the report earlier this year (Scientific Publications: Free for All?) (PDF 118 pages)? The fourteenth report's conclusions are critical of the government, saying that the DTI has sought to neutralise some organisations' views and so prevent significant progress, noting that the government has decided against an author-pays model, and regretting that the government has not taken more decisive action on institutional repositories. The Guardian comments that the government has sided with traditional subscriptions-based publishers. There are more comments in Scitech library questions.

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Public molecules

David Bradley's article in Nature Reviews Drug Discovery 2004, 3, 988 discusses two collections of molecules which are publicly available. PubChem has over over 650 000 entries, whilst Chemical Entities of Biological Interest (CheBI) has less than four thousand entries. CheBI is a freely available dictionary of small molecular entities, whereas PubChem contains the chemical structures of small organic molecules and information on their biological activities.

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X-ray links

This site from the University of Wisconsin's Chemistry library, lists link to X-ray crystallography sites. Other information is available from NIST, RIO-DB, Reciprocal Net, and an Engineering Chemistry Database

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Google Scholar

Google Scholar searches the scientific literature. The American Chemical Society has complained that the name is too similar to their product SciFinder Scholar, even though this searches the Chemical Abstracts database and not the open-access web. Google Scholar may be most useful for those fields for which the open-access literature is key to the subject. Chemistry has so many closed-access journals of importance that Google Scholar appears to give an unbalanced view of the field, at the moment. Slashdot

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SPARC Author's Addendum [PDF]

SPARC is developing a standardized "author's addendum" that researchers and authors will be able to use when submitting journal articles to insure retention of key rights. SPARC is seeking feedback on two draft addenda (PDF), developed by Professor Michael Carroll and representing two different approaches to the problem of balancing the needs of authors, readers, and publishers., an assistant professor at Villanova University School of Law, developed these drafts for SPARC.

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Synthetic Dye Industry History

The United States synthetic dye industry emerged during the early twentieth century, and was the forerunner of the modern chemical industry. Now Robert Baptista, a former Bayer chemist, has started work on a website dealing with the history of the dye industry in the USA.