Systematic Dissociation Pathway Searches Guided by Principal Component Modes.

ABSTRACT: We introduce a novel method, Pathway Search guided by Internal Motions (PSIM), that efficiently finds molecular dissociation pathways of a ligand-receptor system with guidance from principal component (PC) modes obtained from molecular dynamics (MD) simulations. Modeling ligand-receptor dissociation pathways can provide insights into molecular recognition and has practical applications, including understanding kinetic mechanisms and barriers to binding/unbinding as well as design of drugs with desired kinetic properties. PSIM uses PC modes in multilayer internal coordinates to identify natural molecular motions that guide the search for conformational switches and unbinding pathways. The new multilayer internal coordinates overcome problems with Cartesian and classical internal coordinates

SUBMITTER: Tang Z 

PROVIDER: S-EPMC5920795 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature