Let's say we have an inhibitor with known activity, we chose this ligand as a reference. We then tested other ligands at the same active site and looked for protein-ligand interactions. We saw which amino acids it bonds with. My question is: can it be calculated in % how similar the binding site is to the reference with the ligands tested? I saw this calculation in an article (see:screenshot) and couldn't find how it's done. Does anyone have any ideas on how to do it, using which software?
Here's a tool for Protein Pocket Similarity Comparison:
http://proline.physics.iisc.ernet.in/pocketmatch/
Corresponding Publication: Article PocketMatch: A new algorithm to compare binding sites in pro...
@ Naz Mina Mert thank you so much:)) Of course I'm attaching the article now
@Sutanu Mukhopadhyay Thank you very much for your suggestion, but I meant the binding similarity with respect to the standard ligand. The article is available in Table 2.
Here, i believe % of the binding site similarity is calculated by dividing the number of same hydrophobic residues to the respective (standart) ligand (which is 9/4).
Naz Mina Mert Exactly!, Thank you so much, thats so very clever approach.
- Badges
- Science topic
- Similar topics
- Philosophy
- Ethics