Protein folding of the HOP model: A parallel Wang—Landau study

26th IUPAP Conference on Computational Physics

物理学;计算机科学

Shi, G.^1 ; Wüst, T.^2 ; Li, Y.W.^3 ; Landau, D.P.^1

Center for Simulational Physics, University of Georgia, Athens

GA

30602, United States^1

Scientific IT Services, ETH Zürich IT Services, Zürich

8092, Switzerland^2

National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge

TN

37831, United States^3

关键词: Hydrophobic-polar proteins;    Low temperatures;    Replica exchange;    Simple modifications;    Wang-Landau sampling;   

Others  :  https://iopscience.iop.org/article/10.1088/1742-6596/640/1/012017/pdf
DOI  :  10.1088/1742-6596/640/1/012017

学科分类：计算机科学（综合）

来源: IOP

【 摘 要 】

We propose a simple modification to the hydrophobic-polar (HP) protein model, by introducing a new type of monomer, "0", with intermediate hydrophobicity of some amino acids between H and P. With the replica-exchange Wang-Landau sampling method, we investigate some widely studied HP sequences as well as their H0P counterparts and observe that the H0P sequences exhibit dramatically reduced ground state degeneracy and more significant transition signals at low temperature for some thermodynamic properties, such as the specific heat.