Finding pockets and their properties (like, Surface Area) from a PDB file¶

This example shows how to find pockets in an input PDB file using the OEFindPockets function. OEDesignUnit file (OEDesignUnit) can also be used as input to find the pockets.

Command Line Interface¶

This example uses an input PDB file, and will print surface area and list of residues for each found pocket in given PDB file.

prompt> findpockets <input protein molecule or DesignUnit file>

Code¶

Download code

findpockets.py and the 7mhf.pdb (the input PDB file),

Example¶

prompt> findpockets.py 7mhf.pdb

will generate the following output:

pockets count: 1
pocket_1 Residues count:  22
pocket_1 Residues:
HOH 623   A 2
GLY 143   A 1
ASN 142   A 1
HOH 502   A 2
DMS 404   A 2
MET 165   A 1 A
HOH 624   A 2
ASP 187   A 1
HOH 671   A 2
HOH 655   A 2
HOH 589   A 2
MET 49   A 1
HOH 782   A 2
ARG 188   A 1
THR 25   A 1
HIS 41   A 1
GLN 189   A 1
CYS 44   A 1
HOH 750   A 2
HOH 548   A 2
THR 45   A 1
SER 46   A 1
pocket_1 Surface Area:  211.0912322998047