A critical perspective on Markov state model treatments of protein-protein association using coarse-grained simulations.

ABSTRACT: Atomic-level information is essential to explain the specific interactions governing protein-protein recognition in terms of structure and dynamics. Of particular interest is a characterization of the time-dependent kinetic aspects of protein-protein association and dissociation. A powerful framework to characterize the dynamics of complex molecular systems is provided by Markov State Models (MSMs). The central idea is to construct a reduced stochastic model of the full system by defining a set of conformational featured microstates and determining the matrix of transition probabilities between them. While a MSM framework can sometimes be very effective, different combinations of input featurization and simulation methods can significantly affect the robustness and the quality of the infor

SUBMITTER: He Z 

PROVIDER: S-EPMC7902085 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature