The VisGrid algorithm identifies geometric features of protein surfaces using an intuitive concept of the visibility. In our benchmark, VisGrid correctly identified 95.0% of ligand binding sites as one of the three largest pockets in 5616 benchmark proteins.

Binary file from here

./VisGrid <options> <PDB file>
         -r : output pocket residues [default]
         -v : output all voxel points in pockets
         -c : output pocket center
         -a : output all

Example 1: Pocket residues
$ ./VisGrid 1crn.pdb
PDB: 1crn.pdb;
Residues in pocket 1:
7,8,9,10,11,12,15,16,18,19,21,25,29,30,46
Residues in pocket 2:
1,2,3,10,38,40,45,46
Residues in pocket 3:
13,14,17

Example 2: Voxel points
$ ./VisGrid -v 1crn.pdb
Voxels: 468 points in pocket 1
        1.40919 -1.50081 -3.23181
        2.30919 -1.50081 -4.13181
        2.30919 -2.40081 -3.23181
...
Voxels: 156 points in pocket 2
        14.9031 5.92406 6.80405
        14.9031 5.02406 7.70405
        14.9031 7.72406 5.90405
...
Voxels: 99 points in pocket 3
        6.1298 4.9028 -5.4052
        6.1298 4.9028 -4.5052
        7.0298 4.0028 -4.5052
...

Example 3: Pockets center
$ ./VisGrid -c 1crn.pdb
PDB: 1crn.pdb;
Center of gravity: 2.75451 3.73489 4.90202 in pocket 1
Center of gravity: 18.2147 8.60752 9.12361 in pocket 2
Center of gravity: 9.95971 5.38761 0.0434276 in pocket 3

Example 4: Pocket residues and pockets center
$ ./VisGrid -rc 1crn.pdb
PDB: 1crn.pdb;
Residues in pocket 1:
7,8,9,10,11,12,15,16,18,19,21,25,29,30,46
Center of gravity: 2.75451 3.73489 4.90202 in pocket 1

Residues in pocket 2:
1,2,3,10,38,40,45,46
Center of gravity: 18.2147 8.60752 9.12361 in pocket 2

Residues in pocket 3:
13,14,17
Center of gravity: 9.95971 5.38761 0.0434276 in pocket 3

Please cite:
Bin Li, Srinivasan Turuvekere, Manish Agrawal, David La, Karthik Ramani & Daisuke Kihara, Characterization of local geometry of protein surfaces with the visibility criterion, Proteins: Struct. Funct. Bioinformatics, 71: 670-683 (2008)

Copyright of this distribution belongs to Bin Li & Daisuke Kihara. It's free for academic non-profit institutions. For commercial entities or government research labs, please contact us (dkihara@purdue.edu) to get the allowance of using this distribution. Redistribution of any files in this pack without our allowance is prohibited.

If you have any questions or suggestions, please feel free to contact us (dkihara@purdue.edu). This package will be updated based on the user feedback.