Dear Min, There is no software that can accurately calculate the binding energy of a predicted (docking) or solved (X-ray structure) protein-ligand complex particularly for ligands that are different chemically - not part of a congeneric series. While there are a number of publications on methods (LIE, FEP, MD, MMPB(GB)SA, QM/MM, even semi-empirical QM methods) for predicting binding energy, most of these publication show results for congeneric series compounds not chemically diverse ligands which is the result you will get from screening a chemical database with Autodock. There are publications by SP Brown J Chem Inf Model. 2007 Jul-Aug;47(4):1493-503, J Chem Inf Model. 2006 May-Jun;46(3):999-1005 using MMPBSA showing a correlation between predicted and measured binding energy of around 0.8. The 0.8 correlation may not be in the papers but might have only been shown in presentations given by Scott. If you are looking for accurate predictions a 0.8 correlation is not very accurate. If you were thinking about using docking scores, a publication that looked at using docking scores to predict binding energy is Warren et al. J Med Chem 2006, 49, 5912. The last third of this publication showed that using docking scores to predict binding energy was a very bad idea even for congeneric series.
Regards, Greg From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of WEI MIN Sent: Thursday, July 22, 2010 1:51 PM To: [email protected] Subject: [ccp4bb] which software can calculate binding energy Dear All I have been using the Autodock software for docking the drug candidate compounds into the receptor structures. I would like to calculate accurately the binding energy. Would anyone introduce me a software? Any help would be greatly appreciated. Best Min
