Molecular dynamics simulations are used to describe the patterns, strength, and properties of protein behavior, drug-receptor interactions, the solvation of molecules, the conformational changes that a protein or molecule may undergo under various conditions, and other events that require the systematic evaluation of molecular properties in dynamic molecular systems. Only few years ago proteins were considered to be rigid body structures with very limited conformational flexibility. However, it is now clear that proteins are highly dynamic structures, the internal organization of which is the key to their 3D spatial arrangement and hence biological function. The study of protein dynamics in the lab is a very complicated, expensive, and time-consuming process. Therefore, a lot of effort and hope lies with the computers and the in silico study of protein structure and molecular dynamics. Herein, an effort has been made to describe the ever-evolving field of molecular dynamics, the different algorithms, and force fields that are being used as well as to provide some insight on what the near future holds for this auspicious field of computational structural biology.
Keywords: Drug–receptor interactions; Molecular dynamics algorithms; Molecular dynamics force fields; Molecular dynamics simulations; Protein behavior; Protein conformational changes; Solvation of molecules.
© 2014 Elsevier Inc. All rights reserved.
Wallnoefer HG, Liedl KR, Fox T. Wallnoefer HG, et al. J Chem Inf Model. 2011 Nov 28;51(11):2860-7. doi: 10.1021/ci200138u. Epub 2011 Oct 19. J Chem Inf Model. 2011. PMID: 21970362
Meyer T, D'Abramo M, Hospital A, Rueda M, Ferrer-Costa C, Pérez A, Carrillo O, Camps J, Fenollosa C, Repchevsky D, Gelpí JL, Orozco M. Meyer T, et al. Structure. 2010 Nov 10;18(11):1399-409. doi: 10.1016/j.str.2010.07.013. Structure. 2010. PMID: 21070939
Ji C, Mei Y. Ji C, et al. Acc Chem Res. 2014 Sep 16;47(9):2795-803. doi: 10.1021/ar500094n. Epub 2014 Jun 2. Acc Chem Res. 2014. PMID: 24883956
Hug S. Hug S. Methods Mol Biol. 2013;924:127-52. doi: 10.1007/978-1-62703-017-5_6. Methods Mol Biol. 2013. PMID: 23034748 Review.
Paquet E, Viktor HL. Paquet E, et al. Biomed Res Int. 2015;2015:183918. doi: 10.1155/2015/183918. Epub 2015 Feb 16. Biomed Res Int. 2015. PMID: 25785262 Free PMC article. Review.
Zhao Y, Yang H, Wu F, Luo X, Sun Q, Feng W, Ju X, Liu G. Zhao Y, et al. Int J Mol Sci. 2022 Sep 6;23(18):10259. doi: 10.3390/ijms231810259. Int J Mol Sci. 2022. PMID: 36142164 Free PMC article.
Kahana A, Lancet D, Palmai Z. Kahana A, et al. Life (Basel). 2022 Jun 24;12(7):955. doi: 10.3390/life12070955. Life (Basel). 2022. PMID: 35888044 Free PMC article.
Fields C, Glazebrook JF, Levin M. Fields C, et al. Neurosci Conscious. 2021 Aug 2;2021(2):niab013. doi: 10.1093/nc/niab013. eCollection 2021. Neurosci Conscious. 2021. PMID: 34345441 Free PMC article.
Li X, Lin B, Lin Z, Ma Y, Wang Q, Zheng Y, Cui L, Luo H, Luo L. Li X, et al. Sci Rep. 2021 Mar 1;11(1):4901. doi: 10.1038/s41598-021-84380-w. Sci Rep. 2021. PMID: 33649481 Free PMC article.
Zulfiqar Z, Shah FA, Shafique S, Alattar A, Ali T, Alvi AM, Rashid S, Li S. Zulfiqar Z, et al. J Inflamm Res. 2020 Dec 24;13:1185-1205. doi: 10.2147/JIR.S284471. eCollection 2020. J Inflamm Res. 2020. Retraction in: J Inflamm Res. 2022 Nov 07;15:6069-6070. doi: 10.2147/JIR.S395887. PMID: 33384558 Free PMC article. Retracted.