Implementation of Time-Averaged Restraints with UNRES Coarse-Grained Model of Polypeptide Chains.

ABSTRACT: Time-averaged restraints from nuclear magnetic resonance (NMR) measurements have been implemented in the UNRES coarse-grained model of polypeptide chains in order to develop a tool for data-assisted modeling of the conformational ensembles of multistate proteins, intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs), many of which are essential in cell biology. A numerically stable variant of molecular dynamics with time-averaged restraints has been introduced, in which the total energy is conserved in sections of a trajectory in microcanonical runs, the bath temperature is maintained in canonical runs, and the time-average-restraint-force components are scaled up with the length of the memory window so that the restraints affect the simulated s

SUBMITTER: Co NT 

PROVIDER: S-EPMC11823420 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature