Computer Atlas of Surface Topology of Proteins

castp
Developer(s) Joe Dundas and Zheng Ouyang
Type computational software
Alexa rank 16445
Website castp Homepage
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.[1]


Algorithm

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.[2] The core algorithm helps in finding the pocket or cavity with capability of housing a solvent with a diameter of 1.4 Å.[3] Predicting a binding site in a protein is a fundamental step of docking or drug designing. As this tool helps in finding cavity or pockets in the structure it is used for identifying active sites where drugs can bind.

Calculations

It computation are as follows

  1. pockets and cavities are identified analytically,
  2. the boundary between the bulk solvent and the pocket is defined precisely,
  3. all calculated parameters are rotationally invariant, and do not involve discretization and they make no use of dot surface or grid points[4]

The CASTp algorithm is publicly available. This online tool also supports the UCSF Chimera plugin for Molecular Visualisation.

Click here to view a Powerpoint presentation showing to use CASTp.

See also

References

  1. ↑ Search CASTp database
  2. ↑ CASTp: Computed Atlas of Surface Topography of proteins
  3. ↑ Characterizing Protein Structures by Surface Mapping - Elaine Ellen Thompson - Google Books. Books.google.co.in. Retrieved 2013-09-08.
  4. ↑ CASTp background
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