User Manual

POCASA is a program used for prediction of ligand binding sites of protein. Now, the version is 1.1.

Parameters

Grid Size

This parameter determines the size of unit gird in the 3D grid system into which proteins will be mapped. The recommended value is 1Å for most cases.

Probe radius

The input radius should be a nonnegative integer of an empirical range from 1Å to 4Å. The probe sphere with a radius of 2Å is competent for most cases. However, you can still freely change the probe radius. In principle, larger probe spheres are used for large ligands or large flat pockets, while small probe spheres are used for small ligands.

Single Point Flag (SPF)

SPF is used to remove noise points of the search result. The input value should be a nonnegative integer less than 28. The SPF value around 16 or 9 is recommended when the grid size of 1Å or 0.5Å is adopted.

Protein Depth Flag (PDF)

PDF is used to recover the useful pocket points deleted by SPF. The input value should be a nonnegative integer less than 28. The PDF value around 18 and 10 is recommended for 1Å and 0.5Å grid size, respectively.

Top-N

In usual, more than one pocket (cavity) will be found for a target protein. This parameter determines that Top-N ranked pockets and cavities will be output. For most cases, N=5 is recommended. Moreover, when a vale of 0 is specified, all pockets and cavities will be output.

Chain ID

By default parameter "NULL", the first chain in the input pdb file will be used. Also, the chain ID could be designated by users with the following format:
"A", "a,b", "1 2" or "ABC" (input without quotation mark).

Atom Type

User can specify atom type that will be used for pocket/cavity searching. When the atom type is set as "protein", only protein atom will be used. When the atom type is set as "all", all the atoms will be used. However, the parameter of Chain ID is of high priority to the "atom type". According the parameter of China ID, this parameter may not work. If the "Chain ID" is "NULL" by default, only the atoms before the first "TER" mark will be used. Whatever the "atom type" is, the atom lines after the first "TER" will be ignored. If the "Chain ID" is specified by user, for example, "A" or "AB", the "TER" mark will be ignored and the "atom type" will work.

Input

There are two alternative manners to specify the input files:

1. One way is to upload your input files from the local directory, which should include the atom coordinate lines of the same format as the standard PDB files.
   
2. The other one is to input the PDB ID and the program will automatically download it from the PDB website.

Output

XXXX_simple.pdb

This file includes the parts of the input file that POCASA uses for the detection of pockets and cavities. If the results are not those which you want, please first check this file to make sure whether the proper parts are used.

XXXX_Parameters.txt

This file stores the parameters that the users input. The information of predicted pocketed and cavities obtained by POCASA is also stored in this file, including volume, VD value and average VD values. The important information, the rank order of the predicted pockets (cavities) is g Also given in this file.

XXXX_TopN_pockets.pdb

This file stores the atom coordinates of the top N pockets (cavities). The atom coordinate lines are of the same format as that of the standard PDB file. The pocket (cavity) numbers are used as the residue numbers. Each point in pockets (cavities) is represented by a hydrogen atom.

XXXX_PocketCenters.pdb

This file includes the geometric centers of the top N pockets (cavities).