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Calculation Request
CASTp Information
 
About CASTp
Background
Input & output
Examples
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PyMOL plugin
   
About your input:

You can either type the 4 letter PDB code of a protein structure if it is available form Brookhaven protein databank (in this case the CAST server will fetch that structure), or, you can upload a structure to the CAST server for calculation.

The structure of the molecule to be uploaded must be in PDB format. Please take care to remove all nonpolar H atoms, else they will not be recognized and will be assigned a default radius of 1.8 angstrom, which may result in a misleading calculation. This is particularly relevant to NMR structures.

Do not request from PDB or upload a structure that contains multiple conformers, such as those seen in NMR structure. CAST does not know which one to pick. Instead, upload a file containing a single structure of your interest, for example by editing the original file.

All hetero atoms will be treated as ligand and will be automatically removed from calculation. This includes solvent water molecules.


About the calculation:

The calculation uses a solvent probe of radius 1.4 angstrom. Currently, the server does not support any other probe radius, nor van der Waals molecule. In structures solved by NMR, the first model is used for the CASTp calculation.

The atomic radii is based on a version of parameter table used by the electrostatic program UHBD from McCammon group, thanks to Cindy Gibas in Shankar Subramaniam's group.


About the results:

CASTp identifies all pockets and cavities of the protein. It also measures their volume and area analytically. In addition, the number, area, and circumcircle of the mouth openings for each pockeet are also measured. All measurements are given in two values, one for the solvent accessible surface (SA, Richards' surface) and one for the molecular surface (MS, Connolly's surface).

You will receive five files in email fro the calculated results: pocket information file, pocket atoms, mouth atoms, and a script file for visualization using rasmol.

Once you received results in your email, you can go back to CASTp server for further computation of the same protein. You will be offered the option to interactively visualize the computed pocket, after the pocket structures of the protein is computed by an earlier request. This is a great way to explore the surface features of a protein. For example, each time you can check and see if a specific residue is in a pocket and what that pocket looks like.

Pocket Information

We use bovine pancreatic trypsin inhibitor (BPTI, 6pti) as an example. CASTp identifies the following pockets and cavity, along with the measurements. The output looks like:

POC Molecule ID N_mth Area_sa Area_ms Vol_sa Vol_ms Lenth cnr
POC 6pti.nW 1 1 0.034 16.98 0.000 7.16 0.74 3
POC 6pti.nW 2 1 0.631 9.75 0.498 7.55 4.98 3
POC 6pti.nW 3 0 15.644 143.74 1.261 96.25 42.44 38