Chemical Informatics Letters

Volume 7, Issue 6; December 2003

Editor: Jonathan M Goodman

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Molecular Modelling Programs

Last reviewed in Chemical Informatics Letters 2002, 5, #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, 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 not clear when the program was last updated, but the web pages appear to have remained unchanged for several years.
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 July 2003.
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. Last update in June 2003. The main authors are T. Helgaker, H. J. A. Jensen, P. Jorgensen, J. Olsen, K. Ruud, H. Ågren.
FSatom: Free software project for atom scale simulation, which will incorporate Molecular Dynamics and Force Fields, Quantum Chemistry and Density Functional Methods. Last updated October 2003.
GAMESS-UK: Ab initio calculations. Martyn Guest, of the Daresbury Laboratory, is the main author. Last updated April 2003.
GAMESS-US: Ab initio calculations. The program is maintained by Dr Mark Gordon's research group at the Ames Laboratory. Last updated July 2003.
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.
InterChem: Ichmech incorporated in 2001. 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). Updated in June 2002.
MOLPRO: A quantum chemistry package developed by Professor Peter Knowles at Birmingham University and Professor Hans-Joachim Werner at Stuttgart University. Last updated February 2003.
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. Last updated June 2003.
Tinker: A free, full source code (Fortran) molecular mechanics and dynamics program, written in the Ponder Lab. Last updated in September 2003.

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Viewing and Drawing Molecules

Unlike the previous section, these programs appear only to be for drawing and manipulating molecules and not for doing molecular modelling calculations, although it is sometimes unclear exactly what their capabilities are, and some of them describe themselves as 'molecular modelling programs'. There is index of molecular display programs at the Lawrence Livermore National Laboratory, and a another World Index of modelling and visualisation at the San Diego Supercomputer Centre.

Biodesigner: Free program, particularly designed for biomolecules. Last updated July 2002.
Chimera: An 'extensible molecular modelling system' from the Computer Graphics Laboratory at UCSF, and free of charge for academic use, which appears to be limited to visualisation rather than modelling. Last updated in November 2003.
Dino: A 3D visualization program for structural biology data written under X and OpenGL. Last updated in September 2003.
Flo: A molecular modelling program that helps chemist to visualize molecules and aids the design of lead drug compounds. Last updated April 2003.
gOpenMol: A Finnish tool for the visualization and analysis of molecular structures, written in Tcl/Tk, Last updated in September 2003.
Molmol: MOLecule analysis and MOLecule display, for biological molecules, written in the group of Professor Kurt Wüthric. Last updated in January 2003.
O: A protein crystallographic package Last updated in December 2002.
Prepi: A molecular graphics program. Date of last update is unclear.
PyMOL: An open-source 'molecular modelling system' written in Python. The program appears to be designed to display and manipulate molecules. Last updated November 2003.
VMD: Visual Molecular Dynamics, from the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign. Last updated November 2003.

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HSDB

The Hazardous Substance Databank from the NIH is a factual data file with information on the toxicology and handling procedures for over 4500 molecules. PubMed now has LinkOut access to the HSDB, so it is easy to go from an article to toxicology information

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Managing programmers

What is the best way to administer a programming project? Software Reality has an article that argues administrators have become too powerful.

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MolSoft

MolSoft from San Diego is, in its own words: "a primary source of new breakthrough technologies in computational chemistry and biology". It has computational environments for molecular modeling, bioinformatics, cheminformatics and ligand docking.

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Converting printed chemical structures to connection tables

A program that could reliably take an illustration of a molecule and convert it to a structure which could be analysed by molecular modelling and chemical informatics tools would be extremely useful. However, nothing which does this is in general use, which demonstrates that the problem is an extremely challenging one. Probably the best program available is Clide

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Changes for 3D molecules in web sites

The way in which web browsers interpret the tags <object>, <embed> and <applet> is likely to change. More information is available from Microsoft and Apple. This is likely to have a big effect on the display of chemical structures, which often depends on these tags. Instead of just displaying a molecule, the browser will produce a pop-up confirmation window. It is possible to circumvent this problem using Javascript, and the Apple website explains how to do this.

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Semantic Web

The Scientific American has an article by Tim Berners-Lee describing the Semantic Web - a vision of how today's World-Wide-Web could develop into something more powerful: "Now, miraculously, we have the Web. For the documents in our lives, everything is simple and smooth. But for data, we are still pre-Web". Based on Resource Description Frameworks software agents might automatically explore the information available gathering useful information.

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Free Unix

This year is the twentieth anniversary of the start of the GNU project, initiated by Richard Stallman

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Molinspiration

There is a new release of Molinspiration's drugability calculator. This interactive applet allows easy calculation of activity scores for potential GPCR ligands, ion channel modulators and kinase inhibitors.

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Authors from five countries banned from ACS journals

The ACS has imposed a moratorium on papers written by authors in Cuba, Iran, Iraq, Libya or the Sudan. (C&E News - subscribers only) because this could be deemed to violate US trade sanctions against these countries. Robert Bovenschulte, who runs the ACS' Publications Division, said the decision was taken with great reluctance and hopes that this will be temporary.

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ChemWeb

Elsevier has decided not to continue with its web portals: BioMedNet, ChemWeb and Elsevier Engineering. It is to be hoped that the Chemistry Preprint Server will continue. ChemWeb has provided valuable information in an innovative way over the six years of its existence, and been an important force in the development of new ways of communicating chemistry. It will be missed.