Journal ArticleDOI
Monte carlo simulation of a first-order transition for protein folding
Ming-Hong Hao,Harold A. Scheraga +1 more
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This article is published in The Journal of Physical Chemistry.The article was published on 1994-05-01. It has received 180 citations till now. The article focuses on the topics: Dynamic Monte Carlo method & Hybrid Monte Carlo.read more
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Replica-exchange molecular dynamics method for protein folding
Yuji Sugita,Yuko Okamoto +1 more
TL;DR: In this article, a replica-exchange method was proposed to overcome the multiple-minima problem by exchanging non-interacting replicas of the system at several temperatures, which allows the calculation of any thermodynamic quantity as a function of temperature in that range.
Journal ArticleDOI
THEORY OF PROTEIN FOLDING: The Energy Landscape Perspective
TL;DR: The energy landscape theory of protein folding suggests that the most realistic model of a protein is a minimally frustrated heteropolymer with a rugged funnel-like landscape biased toward the native structure.
Journal ArticleDOI
Multidimensional replica-exchange method for free-energy calculations
TL;DR: A new simulation algorithm for free-energy calculations that greatly enhances the sampling of the conformational space and allows accurate calculations of free energy in a wide temperature range from a single simulation run, using the weighted histogram analysis method.
Journal ArticleDOI
Generalized-ensemble algorithms for molecular simulations of biopolymers.
TL;DR: Three new generalized-ensemble algorithms that combine the merits of the multicanonical algorithm, simulated tempering, and replica-exchange method are presented, which are tested with short peptide systems.
Journal ArticleDOI
Coarse-Grained Protein Models and Their Applications
Sebastian Kmiecik,Dominik Gront,Michal Kolinski,Lukasz Wieteska,Lukasz Wieteska,Aleksandra Elzbieta Dawid,Andrzej Kolinski +6 more
TL;DR: An overview of coarse-grained models focusing on their design, including choices of representation, models of energy functions, sampling of conformational space, and applications in the modeling of protein structure, dynamics, and interactions are provided.
Related Papers (5)
Multicanonical ensemble: A new approach to simulate first-order phase transitions.
Bernd A. Berg,Thomas Neuhaus +1 more