Dear Ahmed, it depends on the type of measure that you want to get. The easiest thing that comes to my mind is to compare the volumes of the active sites - in this way you can get the quantitative measure (in cubic angstroms). For this, you can use Schrodinger SiteMap, VOIDOO, etc. You can also compare the sequence similarities of the actives sites (just isolate the key binding residues and check the percent of identical residues).

There is a recent paper on binding site comparison methods, I suggest you go through it:

Article A benchmark driven guide to binding site comparison: An exha...

Dear Sergii,

Thanks so much, this paper is very interesting.

Hi Ahmed,

You can try PocketMatch.

http://proline.physics.iisc.ernet.in/pocketmatch/

Thanks Martiniano Bello

But I tried using PocketMatch (the online server) and didn't get any results although I uploaded the 2 active sites as pdb files. additionally, I tried to download the installation file but I couldn't install it. Is there any tricks in processing??

Thanks in advance

Hi Ahmed,

You can also give a look at IsoMif perhaps for the identification of binding site molecular interaction field similarities :

- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4743630/

- https://github.com/mtthchrtr/IsoMif

Check out the paper "Superpose3D: A Local Structural Comparison Program That Allows for User-Defined Structure Representations"

Good luck

Dear Ahmed, you can also try ASCONA (detects and aligns protein binding site conformations), MultiBand (compares binding pocket similarity by performing multiple alignments of the given binding sites using geometric hashing technique) and CavBase (detects similarities among protein cavities by comparing their 3D property descriptors encoding chemical characteristics of the pockets).

You can check this software for quantitative proteomic analysis ProteoIQ 2.80

http://www.premierbiosoft.com/products/products.html