Zhanglab forum

Is it possible to use COACH to find the active site of a protein by giving it a docked model of a protein pdb?

Yes, you can input the docked model of a protein pdb to COACH server for predicting the active sites. Every protein with PDB format can be input to COACH for finding the active sites. If you have any question, please contact us.

No, COACH is designed to predict protein–ligand binding sites from apo (unbound) or holo (ligand-bound) protein structures, not from docked complexes. Using a docked model may bias or mislead its prediction. It's best to use the original protein PDB without the docked ligand.

MERT YENEN wrote: ↑Mon Aug 19, 2024 3:24 pm Is it possible to use COACH to find the active site of a protein by giving it a docked model of a protein pdb? BLOODMONEY!

COACH will analyze the protein and identify likely binding sites, which you can then compare to your docked ligand’s position. The ligand itself isn’t required for the prediction.