Category Index

Programs not fitting other categories.
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Analysis tools for calculating electrostatic properties of biomolecules.
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This is a collection of tools for molecular biology experiments e.g. PCR, 2D NOE.
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A collection of useful resources for Biomedical, Bioinformatics, and Structural Biology
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A collection of Chemistry Applications (including Organic Chemistry).
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A collection of Physics Applications related to Structural Biology.
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This is a collection of useful web pages that provides information about how to do Molecular Dynamics Simulations.
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A collection of resources related to parallel computing using Supercomputers or Computer Clusters.
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A collection of tools for structure prediction of DNA, RNA and Protein.
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Some software (e.g. CLUSTAL W, GCG) in this section is specific for doing the sequence alignment of proteins and DNA. Others(e.g. GCG, PHYLIP) are for searching for the evolutionary relationship between of gene (or protein) sequence from an organism and that from other organisms. Few such as "ConSurf" is for analysis of Functional Regions in Proteins using Phylogenetic Information.
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The followings are a collection of software for genetic database of various organisms and for handling molecular database.
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The applications in this section are web-based tools that integrates molecular dynamics simulation and visualisation onto the internet for long distance collaboration in structural biology research.
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This is a collection of programs for performing Monte Carlo (MC) statistical mechanics simulations.
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Applications for constructing molecules (or system of molecules) from small organic/inorganic molecules to macromolecules like proteins DNA/RNA and polymers.
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This is a collection of analysis tools for protein such as 3-D structure comparison, binding site identification, noncovalent bond finder, dimensions of pore of an ion channel etc.
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This is a collection of tools for biomolecular structure determination, refinement and analysis from crystallographic or NMR data.
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This is a collection of useful software for Mathematical, Statistical Analysis, Visualisation and even Programming.
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This section contains software for molecular visualization. Most of them are for rendering large biomolecules such as proteins and DNA/RNA from a wide variety of file formats. Some of them are capable of displaying the molecular orbitals or the electron density resulted from ab initio calculations. Some can be used with a web browser as a plug-in.
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This is a collection of the popular force fields used in molecular dynamics simulation e.g. CHARMm and AMBER.
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Applications for docking a small molecule like drug or ligand onto a large molecule such as an enzyme.
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Programs for ab initio or semi-empirical calculation of electronic structure.
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Programs and scripts to read, write, or convert molecular structure and trajectory files. This includes both standalone programs as well as add-on packages for systems such as Matlab and Mathematica.
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Programs which do not fit into other categories. When enough programs of a similar type have fallen into the miscellaneous category, we will consider creating a new category for them.
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Programs or software systems for performing molecular dynamics simulations.
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