Computing Protein-Protein Association Affinity with Hybrid Steered Molecular Dynamics.

ABSTRACT: Computing protein-protein association affinities is one of the fundamental challenges in computational biophysics/biochemistry. The overwhelming amount of statistics in the phase space of very high dimensions cannot be sufficiently sampled even with today's high-performance computing power. In this article, we extend a potential of mean force (PMF)-based approach, the hybrid steered molecular dynamics (hSMD) approach we developed for ligand-protein binding, to protein-protein association problems. For a protein complex consisting of two protomers, P1 and P2, we choose m (≥3) segments of P1 whose m centers of mass are to be steered in a chosen direction and n (≥3) segments of P2 whose n centers of mass are to be steered in the opposite direction. The coordinates of these m + n centers const

SUBMITTER: Rodriguez RA 

PROVIDER: S-EPMC4565455 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature