Literature DB >> 29117698

Note: MSM lag time cannot be used for variational model selection.

Brooke E Husic1, Vijay S Pande1.   

Abstract

The variational principle for conformational dynamics has enabled the systematic construction of Markov state models through the optimization of hyperparameters by approximating the transfer operator. In this note, we discuss why the lag time of the operator being approximated must be held constant in the variational approach.

Year:  2017        PMID： 29117698      PMCID： PMC5669980          DOI： 10.1063/1.5002086

Source DB:  PubMed          Journal:  J Chem Phys        ISSN： 0021-9606            Impact factor:   3.488


  5 in total

1.  Identification of slow molecular order parameters for Markov model construction.

Authors:  Guillermo Pérez-Hernández; Fabian Paul; Toni Giorgino; Gianni De Fabritiis; Frank Noé
Journal:  J Chem Phys       Date:  2013-07-07       Impact factor: 3.488

2.  Efficient maximum likelihood parameterization of continuous-time Markov processes.

Authors:  Robert T McGibbon; Vijay S Pande
Journal:  J Chem Phys       Date:  2015-07-21       Impact factor: 3.488

3.  Variational cross-validation of slow dynamical modes in molecular kinetics.

Authors:  Robert T McGibbon; Vijay S Pande
Journal:  J Chem Phys       Date:  2015-03-28       Impact factor: 3.488

4.  Optimized parameter selection reveals trends in Markov state models for protein folding.

Authors:  Brooke E Husic; Robert T McGibbon; Mohammad M Sultan; Vijay S Pande
Journal:  J Chem Phys       Date:  2016-11-21       Impact factor: 3.488

5.  Modeling molecular kinetics with tICA and the kernel trick.

Authors:  Christian R Schwantes; Vijay S Pande
Journal:  J Chem Theory Comput       Date:  2015-02-10       Impact factor: 6.006
  5 in total
  7 in total

Review 1.  Markov State Models to Elucidate Ligand Binding Mechanism.

Authors:  Yunhui Ge; Vincent A Voelz
Journal:  Methods Mol Biol       Date:  2021

2.  Directed kinetic transition network model.

Authors:  Hongyu Zhou; Feng Wang; Doran I G Bennett; Peng Tao
Journal:  J Chem Phys       Date:  2019-10-14       Impact factor: 3.488

3.  Integrated Variational Approach to Conformational Dynamics: A Robust Strategy for Identifying Eigenfunctions of Dynamical Operators.

Authors:  Chatipat Lorpaiboon; Erik Henning Thiede; Robert J Webber; Jonathan Weare; Aaron R Dinner
Journal:  J Phys Chem B       Date:  2020-10-09       Impact factor: 2.991

4.  Deciphering the Allosteric Process of the Phaeodactylum tricornutum Aureochrome 1a LOV Domain.

Authors:  Hao Tian; Francesco Trozzi; Brian D Zoltowski; Peng Tao
Journal:  J Phys Chem B       Date:  2020-10-01       Impact factor: 2.991

5.  What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models.

Authors:  Ernesto Suárez; Rafal P Wiewiora; Chris Wehmeyer; Frank Noé; John D Chodera; Daniel M Zuckerman
Journal:  J Chem Theory Comput       Date:  2021-04-27       Impact factor: 6.006

6.  Unsupervised Learning Methods for Molecular Simulation Data.

Authors:  Aldo Glielmo; Brooke E Husic; Alex Rodriguez; Cecilia Clementi; Frank Noé; Alessandro Laio
Journal:  Chem Rev       Date:  2021-05-04       Impact factor: 60.622

7.  Determining Sequence-Dependent DNA Oligonucleotide Hybridization and Dehybridization Mechanisms Using Coarse-Grained Molecular Simulation, Markov State Models, and Infrared Spectroscopy.

Authors:  Michael S Jones; Brennan Ashwood; Andrei Tokmakoff; Andrew L Ferguson
Journal:  J Am Chem Soc       Date:  2021-10-13       Impact factor: 15.419
  7 in total

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