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Current Medicinal Chemistry

Editor-in-Chief

ISSN (Print): 0929-8673
ISSN (Online): 1875-533X

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Editorial

The Applications of Molecular Dynamics Simulation in Studying Protein Structure and Dynamics

Author(s): Jingjing Guo and Huanxiang Liu

Volume 31, Issue 20, 2024

Published on: 05 April, 2024

Page: [2839 - 2840] Pages: 2

DOI: 10.2174/092986733120240405144035

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[1]
Zhang, Q.; Zhao, N.; Meng, X.; Yu, F.; Yao, X.; Liu, H. The prediction of protein–ligand unbinding for modern drug discovery. Expert Opin. Drug Discov., 2022, 17(2), 191-205.
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Guo, J.; Zhou, H-X. Protein allostery and conformational dynamics. Chem. Rev., 2016, 116, 6503-6515.
[http://dx.doi.org/10.1021/acs.chemrev.5b00590]
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Klepeis, J.L.; Lindorff-Larsen, K.; Dror, R.O.; Shaw, D.E. Long-timescale molecular dynamics simulations of protein structure and function. Curr. Opin. Struct. Biol., 2009, 19, 120-127.
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[http://dx.doi.org/10.2174/1568026618666181025114157]
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Li, M.; Bao, Y.; Li, M.; Guo, J. GPCR allostery: A view from computational biology. Curr. Med. Chem., 2023, 30, 4533-4553.
[http://dx.doi.org/10.2174/0929867330666230113125246]
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Aci-Sèche, S.; Ziada, S.; Braka, A.; Arora, R.; Bonnet, P. Advanced molecular dynamics simulation methods for kinase drug discovery. Fut. Med. Chem., 2016, 8, 545-566.
[http://dx.doi.org/10.4155/fmc.16.9]
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Wang, L.; Zhang, Q.; Tong, H.H.Y.; Yao, X.; Liu, H.; Li, G. Computational methods for unlocking the secrets of potassium channels: Structure, mechanism, and drug design. Wiley Interdisciplinary Reviews: Comp. Mol. Sci., 2024, 14(1), e1704.
[http://dx.doi.org/10.1002/wcms.1704]
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Barredo, P.A.; Balanay, M.P. Recent advances in molecular dynamics simulations of tau fibrils and oligomers. Membranes, 2023, 13.
[http://dx.doi.org/10.3390/membranes13030277]
[9]
Xu, B.; Chen, Y.; Xue, W. Computational protein design - where it goes? Curr. Med. Chem., 2024, 31(20), 2841-2854.
[http://dx.doi.org/10.2174/0929867330666230602143700]
[10]
Zhong, H.; Liu, H.; Liu, H. Molecular mechanism of tau misfolding and aggregation: Insights from molecular dynamics simulation. Curr. Med. Chem., 2024, 31(20), 2855-2871.
[http://dx.doi.org/10.2174/0929867330666230409145247]
[11]
Shah, S.J.A.; Zhang, Q.; Guo, J.; Liu, H.; Liu, H.; Villà-Freixa, J. Identification of aggregation mechanism of acetylated PHF6* and PHF6 tau peptides based on molecular dynamics simulations and markov state modeling. ACS Chem. Neurosci., 2023, 14, 3959-3971.
[http://dx.doi.org/10.1021/acschemneuro.3c00578]
[12]
Su, J.; Fu, C.; Wang, S.; Chen, X.; Wang, R.; Shi, H.; Li, J.; Wang, X. Screening and activity evaluation of novel BCR-ABL/T315I tyrosine kinase inhibitors. Curr. Med. Chem., 2024, 31(20), 2872-2894.
[http://dx.doi.org/10.2174/0929867330666230519105900]

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