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 |
|
