Structural Biology Software Database
Category Index
367 Applications, 24 CategoriesSort by [ Name | Last Update ]
Miscellaneous (0 entries) |
Programs not fitting other categories. List Entries |
Biomolecular Electrostatic (2 entries) |
Analysis tools for calculating electrostatic properties of biomolecules. List Entries |
Molecular Biology Experimental Tools (4 entries) |
This is a collection of tools for molecular biology experiments e.g. PCR, 2D NOE. List Entries |
Molecular Biology Resources and Databases (28 entries) |
A collection of useful resources for Biomedical, Bioinformatics, and Structural Biology List Entries |
Chemistry Tools (6 entries) |
A collection of Chemistry Applications (including Organic Chemistry). List Entries |
Physics Tools (2 entries) |
A collection of Physics Applications related to Structural Biology. List Entries |
Learning To Do Molecular Dynamics Simulations (1 entry) |
This is a collection of useful web pages that provides information about how to do Molecular Dynamics Simulations. List Entries |
Parallel Computing Resources (7 entries) |
A collection of resources related to parallel computing using Supercomputers or Computer Clusters. List Entries |
DNA, RNA and Protein Stucture Prediction (8 entries) |
A collection of tools for structure prediction of DNA, RNA and Protein. List Entries |
Gene and Protein Sequence Alignment, Phylogenetic Search and Analysis (25 entries) |
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. List Entries |
Genetic Database and Molecular Database Handling (4 entries) |
The followings are a collection of software for genetic database of various organisms and for handling molecular database. List Entries |
Biological Collaboration (2 entries) |
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. List Entries |
Monte Carlo (MC) statistical mechanics simulations (6 entries) |
This is a collection of programs for performing Monte Carlo (MC) statistical mechanics simulations. List Entries |
Molecular Building (18 entries) |
Applications for constructing molecules (or system of molecules) from small organic/inorganic molecules to macromolecules like proteins DNA/RNA and polymers. List Entries |
Protein Structure Analysis and Verification (45 entries) |
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. List Entries |
Crystallography and NMR (32 entries) |
This is a collection of tools for biomolecular structure determination, refinement and analysis from crystallographic or NMR data. List Entries |
Mathematical and Statistical Manipulation (10 entries) |
This is a collection of useful software for Mathematical, Statistical Analysis, Visualisation and even Programming. List Entries |
Molecular Visualization (63 entries) |
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. List Entries |
Molecular Dynamics Force Fields (6 entries) |
This is a collection of the popular force fields used in molecular dynamics simulation e.g. CHARMm and AMBER. List Entries |
Molecular Docking (19 entries) |
Applications for docking a small molecule like drug or ligand onto a large molecule such as an enzyme. List Entries |
Quantum Chemistry Calculation (19 entries) |
Programs for ab initio or semi-empirical calculation of electronic structure. List Entries |
Molecular File Format Conversion (14 entries) |
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. List Entries |
Miscellaneous (12 entries) |
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. List Entries |
Molecular Dynamics (34 entries) |
Programs or software systems for performing molecular dynamics simulations. List Entries |
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