Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques—Searching for Mechanism and Kinetics of Biomolecular Functions

Keywords

Biomolecule, Sampling (signal processing), Replica, Energy landscape, Statistical physics

References

• Cellular Signal Processing: An Introduction to the Molecular Mechanisms of Signal TransductionFriedrich Marks, Ursula Klingmüller, Karin Müller‐Decker — 2008
• Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair昭二 今村, 信一郎 田端, 真 田部 — 2004
• Protein conformational transitions explored by mixed elastic network modelsAshleigh Swingler — 2007
• Disorder-to-order transition of an intrinsically disordered region of sortase revealed by multiscale enhanced sampling.Daniel Marre — 2012
• The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To AskJeffrey Comer, James C. Gumbart, Jérôme Hénin — 2014
• Statistical Physics of Biomolecules: An IntroductionD. Zuckerman — 2010
• An Introduction to Markov State Models and Their Application to Long Timescale Molecular SimulationGregory R. Bowman, Vijay S. Pande, Frank Noé — 2014
• GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulationsJaewoon Jung, Takaharu Mori, Chigusa Kobayashi — 2015
• Relaxation mode analysis and Markov state relaxation mode analysis for chignolin in aqueous solution near a transition temperature.Ayori Mitsutake, Hiroshi Takano — 2015
• The power of coarse graining in biomolecular simulationsHelgi I. Ingólfsson, César A. López, Jaakko J. Uusitalo — 2013
• Ensemble-Biased Metadynamics: A Molecular Simulation Method to Sample Experimental Distributions.Fabrizio Marinelli, José D. Faraldo‐Gómez — 2015
• Multiscale enhanced sampling of intrinsically disordered protein conformationsKuo Hao Lee, Jianhan Chen — 2016
• Diffusion maps, clustering and fuzzy Markov modeling in peptide folding transitions.Lilia V. Nedialkova, Miguel A. Amat, Ioannis G. Kevrekidis — 2014
• Determination of reaction coordinates via locally scaled diffusion map.Mary A. Rohrdanz, Wenwei Zheng, Mauro Maggioni — 2011
• First passage time approach to diffusion controlled reactionsAttila Szabó, Klaus Schulten, Zan Schulten — 1980
• Finding transition pathways using the string method with swarms of trajectories.Albert C. Pan, Deniz Sezer, Benoı̂t Roux — 2008
• Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing.John D. Chodera, Michael R. Shirts — 2011
• Protein Dynamics from Time-Resolved UV Raman SpectroscopyGurusamy Balakrishnan, Colin L. Weeks, Mohammed Ibrahim — 2008
• Markov state models based on milestoning.Christof Schütte, Frank Noé, Jianfeng Lu — 2011
• A quantum generalization of intrinsic reaction coordinate using path integral centroid coordinates.Motoyuki Shiga, Hiroshi Fujisaki — 2012

Cited by

• Energetics and conformational pathways of functional rotation in the multidrug transporter AcrBYasuhiro Matsunaga, Tsutomu Yamane, Tohru Terada — 2017
• Position-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement.Tetsuro Nagai, Shuhei Tsurumaki, Ryo Urano — 2020
• Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques—Searching for Mechanism and Kinetics of Biomolecular FunctionsHiroshi Fujisaki, Kei Moritsugu, Yasuhiro Matsunaga — 2018

Related papers

• RPMSP: A Novel Replica Placement Method Inspired by Self-Similarity Propagation of PlantsXingjia Yuan, Yuelong Zhao — 2019
• OS2609 The revealed matters in the surface observations by the replica methodTerutoshi YAKUSHIJI — 2011
• Research on Replica Strategy in Cloud Storage SystemLin Huo, Ran Yi — 2015
• Validation of the replica trick for simple modelsTakashi Shinzato — 2016
• Free energy landscape of protein-like chains with discontinuous potentials.Hanif Bayat Movahed, Ramses van Zon, Jeremy Schofield — 2011