PocketMatch

Working of this web interface

Two PDB files whose ligands need to be compared are obtained from the upload
Each of the protein files is then processed to extract all ligands and their corresponding site files
All vs All comparison of sites is done with PocketMatch and scores are reported
If there are M ligands/sites in one protein and N in another, then number comparisons is M*N
Grouping of residues is an important factor in computing the score (ref. Paper)

Upload two PDB files whose ligands need to be compared:

PDB1

PDB2

Database vs database comparisons are possible with local installable version of the software
Executable/binaries will be provided upon request from the authors.

Please mail the filled in registration form to the authors to obtain the software Registration form to be mailed to authors
The software is only available for running in linux platforms - however windows users can use Cygwin/or other equivalent softwares on Windows
Linux users - please mention your machine configuration (say output of the command 'uname -a') in the e-mail to authors

Example PDB-1 pdb10gs.ent
Example PDB-2 pdb11gs.ent

Download PocketMatch (version 2.0) (unpublished) source code:

Reference : PocketMatch: A new algorithm to compare binding sites in protein structures (Kalidas Yeturu and Nagasuma Chandra, 2008)