Bioinformatics and Molecular Structure Software

This page has links to other indexes of software you can obtain from the internet to perform analysis on your own machine. This can be a useful way to do work, since it does not depend on the availability of the network. Many personal computers are now powerful enough to perform much of the processing you require. There is also a local list of molecular structure visualisation software.

Indexes at other sites

• EBI BioCatalog A catalogue of bioinformatics software maintained by the European Bioinformatics Institute.
• Biology software for Windows NT/2000 A limited selection
• WWW Computational Chemistry Resources Good set of links
• Software for structure determination and analysis Excellent list at RCSB (new home of PDB) including packages for structure determination using crystallographic and NMR data.

Selected Molecular Structure Visualisation Software Index

Many of these packages can be used to view protein structures from the Molecular Structure Database, held at EBI.

• Chime is a plug-in module for browsers for structure viewing. Often used in on-line tutorials.
• Kinemages and MAGE
• MidasPlus Molecular display and simulation
• MolMol Display and analysis, especially for NMR. (Unix and Windows NT)
• MolScript generates PostScript and a range of other format output from PDB data. (Mole doc: link to home page)
• O Important protein crystallography package.
• PovRay Persistence of Vision Ray-tracing software, many platforms
• Rasmol (manual on mole) and home Most platforms.
• Raster3D generates high quality raster images from PDB files. Available for various flavours of UNIX.
• SWISS-PdbViewer Can analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts.
• Visual Molecular Dynamics Can be web helper. Make/playback MD movies.
• WHAT IF. Protein structure analysis. Costs $250 for an academic licence.