Multi-Self-Overlap Ensemble for protein folding: ground state search and thermodynamics

TL;DR

This paper introduces the Multi-Self-Overlap Ensemble Monte Carlo method for efficiently finding ground states and analyzing thermodynamics of long-chain HP lattice proteins, revealing multiple phase transitions.

Contribution

The authors develop and apply MSOE to successfully identify lowest energy states and study thermodynamics in long-chain HP proteins, achieving results not previously reported.

Findings

MSOE finds lowest energy states for chains of length 42 to 100.

Two successive transitions observed between native and coil states.

Ground state degeneracy influences transition order.

Abstract

Long chains of the HP lattice protein model are studied by the Multi-Self-Overlap Ensemble(MSOE) Monte Carlo method, which was developed recently by the authors. MSOE successfully finds the lowest energy states reported before for sequences of the chain length $N=42\sim 100$ in two and three dimensions. Moreover, MSOE realizes the lowest energy state that ever found in a case of N=100. Finite-temperature properties of these sequences are also investigated by MSOE. Two successive transitions are observed between the native and random coil states. Thermodynamic analysis suggests that the ground state degeneracy is relevant to the order of the transitions in the HP model.