Trypsin-Ligand binding affinities calculated using an effective interaction entropy method under polarized force field.

ABSTRACT: Molecular dynamics (MD) simulation in the explicit water is performed to study the interaction mechanism of trypsin-ligand binding under the AMBER force field and polarized protein-specific charge (PPC) force field combined the new developed highly efficient interaction entropy (IE) method for calculation of entropy change. And the detailed analysis and comparison of the results of MD simulation for two trypsin-ligand systems show that the root-mean-square deviation (RMSD) of backbone atoms, B-factor, intra-protein and protein-ligand hydrogen bonds are more stable under PPC force field than AMBER force field. Our results demonstrate that the IE method is superior than the traditional normal mode (Nmode) method in the calculation of entropy change and the calculated binding free energy unde

SUBMITTER: Cong Y 

PROVIDER: S-EPMC5735144 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature