I’m new to protein-protein docking. I have started to use autodock to predict binding site. But I have no idea how to identify which residues will have interaction with other amino acids on another protein from autodock outcome. And I have tried to use website like zdock or cluspro,they will provide the results in pdb file format. But I still don’t know how to read the result from cluspro to know which amino acids have interaction. And how do I know which interaction it is between the amino acids from those results,such as hydrogen bond,ven der waal force,electrostatics or hydrophobic interaction,etc.
Li-Chung Kuo
LigPlot+ is a good program to start with:
https://www.ebi.ac.uk/thornton-srv/software/LigPlus/
This program has two "modules".. one of them is called DIMPLOT which plot protein-protein or domain-domain interactions. This module will do exactly what you asking for by giving you a 2D diagram of the interface interacions...
hope this helps...
Firstly, you extract the structures obtained from docking.
Then, you use it as the input structure and load it with software such as discovery studio (very nice and free for academic users) or schoedinger. There are some modules for checking the protein-ligand interactions and you can get interaction maps and other analyses.
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