Nonaffine Displacements Encode Collective Conformational Fluctuations in Proteins-Reference-Cited by-同舟云学术

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Nonaffine Displacements Encode Collective Conformational Fluctuations in Proteins

Published:2020-03-24 Issue:4 Volume:16 Page:2508-2516
ISSN:1549-9618
Container-title:Journal of Chemical Theory and Computation
language:en
Short-container-title:J. Chem. Theory Comput.

Author:

Prakashchand Dube Dheeraj¹,Ahalawat Navjeet¹²^ORCID,Bandyopadhyay Satyabrata¹,Sengupta Surajit¹,Mondal Jagannath¹^ORCID

Affiliation:

1. Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500107, India

2. Department of Molecular Biology, Biotechnology and Bioinformatics, Chaudhary Charan Singh Haryana Agricultural University, Hisar 125004, India

Funder

Science and Engineering Research Board

Tata Institute of Fundamental Research

Department of Science and Technology, Ministry of Science and Technology

Publisher

American Chemical Society (ACS)

Subject

Physical and Theoretical Chemistry,Computer Science Applications

Link

https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.9b01100

Reference44 articles.

1. Identification of simple reaction coordinates from complex dynamics

2. Escaping free-energy minima

3. A variational conformational dynamics approach to the selection of collective variables in metadynamics

4. Refining Collective Coordinates and Improving Free Energy Representation in Variational Enhanced Sampling

5. tICA-Metadynamics: Accelerating Metadynamics by Using Kinetically Selected Collective Variables

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1. Nonaffinity of Liquid Networks and Bicontinuous Mesophases;Physical Review Letters;2024-05-23

2. The physical logic of protein machines;Journal of Statistical Mechanics: Theory and Experiment;2024-02-08

3. The Physical Logic of Protein Machines;2023-11-17

4. A deep autoencoder framework for discovery of metastable ensembles in biomacromolecules;The Journal of Chemical Physics;2021-09-21

5. Fundamental Challenges and Outlook in Simulating Liquid–Liquid Phase Separation of Intrinsically Disordered Proteins;The Journal of Physical Chemistry Letters;2021-02-08

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