I need to find a software which could list me the amino acids list of predicted binding site? The big advantage would be if it could divide the enzyme cavity to the specific pockets. Do you know any best?
All best
Michal
The best software to analyze the binding site and interaction is Chimera. If you docked or stimulated your binding, you can use this program to study the residues that are involved in the reaction.
Reza Yekta but can Chimera list it automaticaly without docking? For example I would use the one of emzymes include in my studies. The aminopeptidase N has P1 pocket built by hydrophobic amino acids such as phenylalanines, then there is metal binding motif and next P1' position. I need to list the amino acids building P1' but not after manual studies. The perfect would be prediction with software which could recognize P1 and P1' not only the ligand biding volume or specific Aa in ligand such it is describes in MEROPS database.
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