Computer Atlas of Surface Topology of Proteins
|Developer(s)||Joe Dundas and Zheng Ouyang|
|As of||10 May 2014|
(CASTp) or Computer Atlas of Surface Topology of Proteins, is a tool in Bioinformatics which is an online resource for identifying some of the geometric properties of protein like locating, delineating and measuring concave surface regions on 3D structures of proteins obtained from PDB also to study surface features, functional regions and active site of proteins. there is also measurement of the number of mouth openings(of pocket), area of the openings(of pocket), circumference of mouth opening(of pocket), in both solvent accessible(SA) and Molecular surface(MS) of each pocket. The pocket which does not have any opening to the outside is called cavity(void), it doesn't have any opening for the solvent probe. This server is maintained by University of Illinois at Chicago UIC.
The measurement includes the area and volume of pocket or void as well as measurement of numbers of mouth opening of a particular pocket ID by solvent accessible surface model (Richards' surface) and by molecular surface model (Connolly's surface), all calculated analytically. The core algorithm helps in finding the pocket or cavity with capability of housing a solvent with a diameter of 1.4 Å. Predicting a binding site in a protein is a fundamental step of docking or drug designing. As this tool hepls in finding cavity or pockets in the structure it is used for identifying active sites where drugs can bind.
It computation are as follows
- pockets and cavities are identified analytically,
- the boundary between the bulk solvent and the pocket is defined precisely,
- all calculated parameters are rotationally invariant, and do not involve discretization and they make no use of dot surface or grid points
Click here to view a Powerpoint presentation showing to use CASTp.
- secondary protein structure prediction by psipred
- secondary protein structure prediction by jpred
- Drug design
- Molecular mechanics
- Protein design
- Search CASTp database
- CASTp: Computed Atlas of Surface Topography of proteins
- Characterizing Protein Structures by Surface Mapping - Elaine Ellen Thompson - Google Books. Books.google.co.in. Retrieved 2013-09-08.
- CASTp background