Literature DB >> 26580029

Comparison between Mean Forces and Swarms-of-Trajectories String Methods.

Luca Maragliano1, Benoît Roux1,2, Eric Vanden-Eijnden3.   

Abstract

The original formulation of the string method in collective variable space is compared with a recent variant called string method with swarms-of-trajectories. The assumptions made in the original method are revisited and the significance of the minimum free energy path (MFEP) is discussed in the context of reactive events. These assumptions are compared to those made in the string method with swarms-of-trajectories, and shown to be equivalent in a certain regime: in particular an expression for the path identified by the swarms-of-trajectories method is given and shown to be closely related to the MFEP. Finally, the algorithmic aspects of both methods are compared.

Entities:  

Year:  2014        PMID: 26580029      PMCID: PMC6980172          DOI: 10.1021/ct400606c

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  25 in total

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Authors:  Peter G Bolhuis; David Chandler; Christoph Dellago; Phillip L Geissler
Journal:  Annu Rev Phys Chem       Date:  2001-10-04       Impact factor: 12.703

2.  Finite temperature string method for the study of rare events.

Authors:  Weinan E; Weiqing Ren; Eric Vanden-Eijnden
Journal:  J Phys Chem B       Date:  2005-04-14       Impact factor: 2.991

3.  Finding transition pathways using the string method with swarms of trajectories.

Authors:  Albert C Pan; Deniz Sezer; Benoît Roux
Journal:  J Phys Chem B       Date:  2008-02-22       Impact factor: 2.991

4.  Atomistic view of the conformational activation of Src kinase using the string method with swarms-of-trajectories.

Authors:  Wenxun Gan; Sichun Yang; Benoît Roux
Journal:  Biophys J       Date:  2009-08-19       Impact factor: 4.033

5.  Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI.

Authors:  Victor Ovchinnikov; Martin Karplus; Eric Vanden-Eijnden
Journal:  J Chem Phys       Date:  2011-02-28       Impact factor: 3.488

6.  The free energy landscape analysis of protein (FIP35) folding dynamics.

Authors:  Sergei V Krivov
Journal:  J Phys Chem B       Date:  2011-10-03       Impact factor: 2.991

7.  How conformational dynamics of DNA polymerase select correct substrates: experiments and simulations.

Authors:  Serdal Kirmizialtin; Virginia Nguyen; Kenneth A Johnson; Ron Elber
Journal:  Structure       Date:  2012-04-03       Impact factor: 5.006

8.  All-atom empirical potential for molecular modeling and dynamics studies of proteins.

Authors:  A D MacKerell; D Bashford; M Bellott; R L Dunbrack; J D Evanseck; M J Field; S Fischer; J Gao; H Guo; S Ha; D Joseph-McCarthy; L Kuchnir; K Kuczera; F T Lau; C Mattos; S Michnick; T Ngo; D T Nguyen; B Prodhom; W E Reiher; B Roux; M Schlenkrich; J C Smith; R Stote; J Straub; M Watanabe; J Wiórkiewicz-Kuczera; D Yin; M Karplus
Journal:  J Phys Chem B       Date:  1998-04-30       Impact factor: 2.991

9.  Minimum free energy path of ligand-induced transition in adenylate kinase.

Authors:  Yasuhiro Matsunaga; Hiroshi Fujisaki; Tohru Terada; Tadaomi Furuta; Kei Moritsugu; Akinori Kidera
Journal:  PLoS Comput Biol       Date:  2012-06-07       Impact factor: 4.475

10.  Intermediate state trapping of a voltage sensor.

Authors:  Jérôme J Lacroix; Stephan A Pless; Luca Maragliano; Fabiana V Campos; Jason D Galpin; Christopher A Ahern; Benoît Roux; Francisco Bezanilla
Journal:  J Gen Physiol       Date:  2012-12       Impact factor: 4.086

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  13 in total

1.  The allosteric switching mechanism in bacteriophage MS2.

Authors:  Matthew R Perkett; Dina T Mirijanian; Michael F Hagan
Journal:  J Chem Phys       Date:  2016-07-21       Impact factor: 3.488

Review 2.  Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.

Authors:  Tatiana Maximova; Ryan Moffatt; Buyong Ma; Ruth Nussinov; Amarda Shehu
Journal:  PLoS Comput Biol       Date:  2016-04-28       Impact factor: 4.475

Review 3.  Computational membrane biophysics: From ion channel interactions with drugs to cellular function.

Authors:  Williams E Miranda; Van A Ngo; Laura L Perissinotti; Sergei Yu Noskov
Journal:  Biochim Biophys Acta Proteins Proteom       Date:  2017-08-26       Impact factor: 3.036

4.  A minimization principle for transition paths of maximum flux for collective variables.

Authors:  Robert D Skeel; Ruijun Zhao; Carol Beth Post
Journal:  Theor Chem Acc       Date:  2016-12-21       Impact factor: 1.702

5.  The Activation of c-Src Tyrosine Kinase: Conformational Transition Pathway and Free Energy Landscape.

Authors:  Mikolai Fajer; Yilin Meng; Benoît Roux
Journal:  J Phys Chem B       Date:  2016-10-28       Impact factor: 2.991

6.  A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls.

Authors:  Haochuan Chen; Dylan Ogden; Shashank Pant; Wensheng Cai; Emad Tajkhorshid; Mahmoud Moradi; Benoît Roux; Christophe Chipot
Journal:  J Chem Theory Comput       Date:  2022-02-09       Impact factor: 6.006

7.  Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides.

Authors:  Lev Levintov; Harish Vashisth
Journal:  Biophys J       Date:  2021-10-26       Impact factor: 4.033

8.  Computational methods and theory for ion channel research.

Authors:  C Guardiani; F Cecconi; L Chiodo; G Cottone; P Malgaretti; L Maragliano; M L Barabash; G Camisasca; M Ceccarelli; B Corry; R Roth; A Giacomello; B Roux
Journal:  Adv Phys X       Date:  2022

9.  QM/MM free energy simulations: recent progress and challenges.

Authors:  Xiya Lu; Dong Fang; Shingo Ito; Yuko Okamoto; Victor Ovchinnikov; Qiang Cui
Journal:  Mol Simul       Date:  2016-07-05       Impact factor: 2.178

Review 10.  Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review.

Authors:  Hiroshi Fujisaki; Kei Moritsugu; Yasuhiro Matsunaga; Tetsuya Morishita; Luca Maragliano
Journal:  Front Bioeng Biotechnol       Date:  2015-09-03
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