Coarse-Grained Directed Simulation.

ABSTRACT: Many free-energy sampling and quantum mechanics/molecular mechanics (QM/MM) computations on protein complexes have been performed where, by necessity, a single component is studied isolated in solution while its overall configuration is kept in the complex-like state by either rigid restraints or harmonic constraints. A drawback in these studies is that the system's native fluctuations are lost, both due to the change of environment and the imposition of the extra potential. Yet, we know that having both accurate structure and fluctuations is likely crucial to achieving correct simulation estimates for the subsystem within its native larger protein complex context. In this work, we provide a new approach to this problem by drawing on ideas developed to incorporate experimental information

SUBMITTER: Hocky GM 

PROVIDER: S-EPMC5649387 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature