Molecular modeling
Molecular modeling is one of the important disciplines of bioinformatics.
The latest development of both hardware and software make it possible for
molecular visualization which is fundamental for molecular modeling. Currently,
there are quite few plugins for the real time display and manipulation of
three-dimensional structures with Internet browsers such as Jmol and WebMol
provided in the PDB web server. You may also install standalone tools on
your PC such as Siwss-PDB Viewer and PyMol which have more functionalities.
On the other hand, homology based protein modeling web servers may help
you to predict the three dimensional structure of your protein based on
sequence similarity between your protein and the templates with known 3D
structures.
Visualization and modeling tools
- Swiss-PDB Viewer - A comprehensive
molecular visualization and modeling package developed by Nicolas Guex
at GlaxoSmithKline. It provides a graphical interface and a user friendly
control panel for users to analyze several proteins at the same time.
There are lots useful functions such as superimposition, mutation and
energy minimization for simple molecular simulations.
- PyMol - The home page of
the molecular visualization system written in Python . It is a user sponsored
open source software maintained by DeLano Scientific LLC.
- Cn3D
- The web page of the molecular visualization program Cn3D developed and
distributed by NCBI. It can be installed on your PC to display the three-dimensional
structures obtained from the NCBI MMDB database.
- Kinemage - The home
page of the protein visualization package Kinemage developed and maintained
at the laboratory of Jane Richardson and David Richardson, Duke University.
- RasMol - The home
page of molecular visualization freeware RasMol, maintained by University
of Massachusetts Amherst.
Protein modeling web servers
- Swiss Model - The home
page of the automated comparative protein modeling server, hosted by University
of Basel and the Swiss Institute of Bioinformatics. Extensive documentation
and help materials are provided.
- 3D Jigsaw
- The web server to build three-dimensional models for protein molecules
based on homologues of known structure, developed and maintained by Cancer
Research UK.
- CASP - The entry
page for the international protein structure prediction center, hosted
at University of California at Davies. It provides the means of objective
testing of evaluation of different methods in protein structure prediction.
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| 16 July 2008, J Luo, CBI, PKU, Beijing, China