Comparison of binding affinity evaluations for FKBP ligands with state-of-the-art computational methods: FMO, QM/MM, MM-PB/SA and MP-CAFEE approaches

Abstract

We compared binding affinity evaluations for 10 FKBP ligands with such state-of-the-art computational methods as FMO, QM/MM, MM-PB/SA, and MP-CAFEE. For the FKBP ligands, we confirmed that each method could provide good correlations between the experimental and computational binding affinities. From the calculated results, we discussed the importance of solvation effect and structural sampling for these methods in detail. In addition, we addressed the issues of computational time and present arguments on the future perspective of the computational binding affinity evaluations. © 2010 Chem-Bio Informatics Society.