A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins.

ABSTRACT: Monte Carlo simulations are a powerful technique and are widely used in different fields. When applied to complex molecular systems with long chains, such as those in synthetic polymers and proteins, they have the advantage of providing a fast and computationally efficient way to sample equilibrium ensembles and calculate thermodynamic and structural properties under desired conditions. Conformational Monte Carlo techniques employ a move set to perform the transitions in the simulation Markov chain. While accepted conformations must preserve the sequential bonding of the protein chain model and excluded volume among its units, the moves themselves may take the chain across itself. We call this a break in linear topology preservation. In this manuscript, we show, using simple protein models

SUBMITTER: Especial JNC 

PROVIDER: S-EPMC9695063 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature