Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir-Reference-Cited by-同舟云学术

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Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir

Published:2022-05-03 Issue:6 Volume:18 Page:3930-3947
ISSN:1549-9618
Container-title:Journal of Chemical Theory and Computation
language:en
Short-container-title:J. Chem. Theory Comput.

Author:

Lam Kenneth¹²,Kasavajhala Koushik³²,Gunasekera Sarah⁴,Simmerling Carlos¹³²^ORCID

Affiliation:

1. Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York 11794, United States

2. Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States

3. Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, United States

4. Program in Biology, Stony Brook University, Stony Brook, New York 11794, United States

Funder

National Institute of General Medical Sciences

Publisher

American Chemical Society (ACS)

Subject

Physical and Theoretical Chemistry,Computer Science Applications

Link

https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.2c00065

Reference80 articles.

1. The emerging role of microRNAs in cardiovascular disease

2. RNA in cancer

3. RNA regulatory processes in RNA virus biology

4. mRNA vaccines for infectious diseases: principles, delivery and clinical translation

5. The Protein Data Bank

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1. Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment;Journal of Chemical Information and Modeling;2024-07-13

2. Protein Retrieval via Integrative Molecular Ensembles (PRIME) through Extended Similarity Indices;Journal of Chemical Theory and Computation;2024-07-09

3. Dynamics and Function of sRNA/mRNAs Under the Scrutiny of Computational Simulation Methods;Methods in Molecular Biology;2024

4. van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD;Journal of Chemical Theory and Computation;2023-12-29

5. Rapid Rescoring and Refinement of Ligand–Receptor Complexes Using Replica Exchange Molecular Dynamics with a Monte Carlo Pose Reservoir;Journal of Chemical Theory and Computation;2023-10-13

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