Absolute binding free energies of ligands for pharmaceutical target proteins were calculated by massively parallel method (MP-CAFEE) using new torsion parameters of protein backbone, which were derived with high level ab initio calculations for model molecules of glycine and alanine dipeptides.[1,2]  The new backbone torsion has smaller potential barrier between lower energy structures of glycine than the traditional force fields like AMBER and OPLS-AA. This difference significantly affects the absolute binding energy for the pharmaceutical target proteins like Prion and HIV protease.[1] Fujitani et al.  JPhys. Rev. E 79, 21914 (2009)     [2] Fujitani et al. JCTC 5, 1155 (2009)

Ligand affinity calculations with new torsion parameters of protein backbone

239th National Meeting (2010)

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