Enhanced Coarse-Grained Molecular Dynamics Simulation with a Smoothed Hybrid Potential Using a Neural Network Model-Reference-Cited by-同舟云学术

Enhanced Coarse-Grained Molecular Dynamics Simulation with a Smoothed Hybrid Potential Using a Neural Network Model

Published:2023-12-26 Issue:1 Volume:20 Page:7-17
ISSN:1549-9618
Container-title:Journal of Chemical Theory and Computation
language:en
Short-container-title:J. Chem. Theory Comput.

Author:

Kanada Ryo¹^ORCID,Tokuhisa Atsushi¹^ORCID,Nagasaka Yusuke²,Okuno Shingo²^ORCID,Amemiya Koichiro²,Chiba Shuntaro¹^ORCID,Bekker Gert-Jan³^ORCID,Kamiya Narutoshi⁴^ORCID,Kato Koichiro⁵⁶^ORCID,Okuno Yasushi¹⁷

Affiliation:

1. RIKEN Center for Computational Science, Kobe 650-0047, Japan

2. Fujitsu Limited, Kawasaki 211-8588, Japan

3. Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan

4. Graduate School of Information Science, University of Hyogo, Kobe, Hyogo 650-0047, Japan

5. Graduate School of Engineering, Kyushu University, Fukuoka 819-0395, Japan

6. Center for Molecular System, Kyushu University, 744 Motooka, Noshi-ku, Fukuoka 819-0395, Japan

7. Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan

Funder

Ministry of Education, Culture, Sports, Science and Technology

Japan Society for the Promotion of Science

FOCUS Establishing Supercomputing Center of Excellence project

Publisher

American Chemical Society (ACS)

Subject

Physical and Theoretical Chemistry,Computer Science Applications

Link

https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.3c00889

Reference34 articles.

1. Anton, a special-purpose machine for molecular dynamics simulation

2. Switching of myosin-V motion between the lever-arm swing and Brownian search-and-catch

3. CafeMol: A Coarse-Grained Biomolecular Simulator for Simulating Proteins at Work

4. Topological and energetic factors: what determines the structural details of the transition state ensemble and “en-route” intermediates for protein folding? an investigation for small globular proteins

5. Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations

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