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:



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

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

Download PocketMatch (version 2.1) Executables:

Download PocketMatch (version 2.0) Executables:

Reference 1: PocketMatch: A new algorithm to compare binding sites in protein structures (Kalidas Yeturu and Nagasuma Chandra, 2008)

Reference 2: Nagarajan, D., & Chandra, N. (2013, February). PocketMatch (version 2.0): A parallel algorithm for the detection of structural similarities between protein ligand binding-sites. In Parallel Computing Technologies (PARCOMPTECH), 2013 National Conference on (pp. 1-6). IEEE.