Re-Balancing Replica Exchange with Solute Tempering for Sampling Dynamic Protein Conformations.

ABSTRACT: Replica exchange with solute tempering (REST) is a highly effective variant of replica exchange for enhanced sampling in explicit solvent simulations of biomolecules. By scaling the Hamiltonian for a selected "solute" region of the system, REST effectively applies tempering only to the degrees of freedom of interest but not the rest of the system ("solvent"), allowing fewer replicas for covering the same temperature range. A key consideration of REST is how the solute-solvent interactions are scaled together with the solute-solute interactions. Here, we critically evaluate the performance of the latest REST2 protocol for sampling large-scale conformation fluctuations of intrinsically disordered proteins (IDPs). The results show that REST2 promotes artificial protein conformational collapse

SUBMITTER: Zhang Y 

PROVIDER: S-EPMC10795075 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature