Treffer: Molecular dynamics simulations of proteins: an in-depth review of computational strategies, structural insights, and their role in medicinal chemistry and drug development.
Title:
Molecular dynamics simulations of proteins: an in-depth review of computational strategies, structural insights, and their role in medicinal chemistry and drug development.
Authors:
Farhadi B; EIT Data Science and Communication College, Zhejiang Yuexiu University, Shaoxing, China. 20242705@zyufl.edu.cn., Beygisangchin M; Research Laboratory for Analytical Instrument and Electrochemistry Innovation, Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand. m.beygi2300@gmail.com.; Research Laboratory on Advanced Materials for Sensor and Biosensor Innovation, Materials Science Research Center, Center of Excellence for Innovation in Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand. m.beygi2300@gmail.com., Ghamari N; Department of Biology, School of Sciences, Razi University, Baq-e-Abrisham, Kermanshah, 6714967346, I.R. of Iran., Jakmunee J; Research Laboratory for Analytical Instrument and Electrochemistry Innovation, Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand.; Research Laboratory on Advanced Materials for Sensor and Biosensor Innovation, Materials Science Research Center, Center of Excellence for Innovation in Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand., Tang T; EIT Data Science and Communication College, Zhejiang Yuexiu University, Shaoxing, China.
Source:
Biological cybernetics [Biol Cybern] 2025 Sep 26; Vol. 119 (4-6), pp. 28. Date of Electronic Publication: 2025 Sep 26.
Publication Type:
Journal Article; Review
Language:
English
Journal Info:
Publisher: Springer Verlag Country of Publication: Germany NLM ID: 7502533 Publication Model: Electronic Cited Medium: Internet ISSN: 1432-0770 (Electronic) Linking ISSN: 03401200 NLM ISO Abbreviation: Biol Cybern Subsets: MEDLINE
Imprint Name(s):
Publication: Berlin : Springer Verlag
Original Publication: Berlin, New York, Springer-Verlag.
Original Publication: Berlin, New York, Springer-Verlag.
MeSH Terms:
References:
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Grant Information:
Fundamental Fund 2025 Chiang Mai University and Center of Excellence for Innovation in Chemistry. Partially supported by CMU Proactive Researcher Scheme (2024), Chiang Mai University; Fundamental Fund 2025 Chiang Mai University and Center of Excellence for Innovation in Chemistry. Partially supported by CMU Proactive Researcher Scheme (2024), Chiang Mai University
Contributed Indexing:
Keywords: Biomolecules; Drug design; Inhibitor development; Molecular dynamic simulations; Proteins
Substance Nomenclature:
0 (Proteins)
Entry Date(s):
Date Created: 20250926 Date Completed: 20250926 Latest Revision: 20251210
Update Code:
20251210
DOI:
10.1007/s00422-025-01026-0
PMID:
41003729
Database:
MEDLINE
Weitere Informationen
Molecular dynamics (MD) simulations have emerged as a powerful and extensively employed tool in biomedical research, offering insights into intricate biomolecular processes such as structural flexibility and molecular interactions, and playing a pivotal role in the development of therapeutic approaches. Although MD techniques are applied to a variety of biomolecules including DNA, RNA, proteins, and their assemblies, this review focuses specifically on the role of MD in elucidating protein behavior and their interactions with inhibitors across different disease contexts. The selection of an appropriate force field is essential, as it greatly influences the reliability of simulation outcomes. Widely adopted MD software packages such as GROMACS, DESMOND, and AMBER leverage rigorously tested force fields and have shown consistent performance across diverse biological applications. Despite current successes, challenges remain in narrowing the gap between computational models and actual cellular conditions. The integration of machine learning and deep learning technologies is expected to accelerate progress in this evolving field.
(© 2025. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
Declarations. Competing interests: The authors declare no competing interests.