Molecular dynamics, monte carlo simulations, and langevin dynamics: a computational review

BioMed Research International
Eric Paquet, Herna L Viktor

Abstract

Macromolecular structures, such as neuraminidases, hemagglutinins, and monoclonal antibodies, are not rigid entities. Rather, they are characterised by their flexibility, which is the result of the interaction and collective motion of their constituent atoms. This conformational diversity has a significant impact on their physicochemical and biological properties. Among these are their structural stability, the transport of ions through the M2 channel, drug resistance, macromolecular docking, binding energy, and rational epitope design. To assess these properties and to calculate the associated thermodynamical observables, the conformational space must be efficiently sampled and the dynamic of the constituent atoms must be simulated. This paper presents algorithms and techniques that address the abovementioned issues. To this end, a computational review of molecular dynamics, Monte Carlo simulations, Langevin dynamics, and free energy calculation is presented. The exposition is made from first principles to promote a better understanding of the potentialities, limitations, applications, and interrelations of these computational methods.

References

Sep 1, 1994·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·S Toxvaerd
Jan 6, 1992·Physical Review Letters·U EichmannW Sandner
Apr 6, 1992·Physical Review Letters·P H FramptonT J Weiler
Oct 6, 2001·Science·D Baker, A Sali
Jan 22, 2004·Journal of Computational Chemistry·Emilio Gallicchio, Ronald M Levy
Apr 20, 2004·Current Opinion in Structural Biology·Michael Feig, Charles L Brooks
Jul 21, 2006·The Journal of Physical Chemistry. B·Alessandro LaioMichele Parrinello
Oct 25, 2006·The Journal of Chemical Physics·Sergei Izvekov, Gregory A Voth
May 13, 1983·Science·S KirkpatrickM P Vecchi
Feb 5, 2008·EMBO Reports·Guy G DodsonChandra S Verma
May 16, 2009·Journal of Computational Chemistry·B R BrooksM Karplus
Jul 6, 2010·Proteins·Morgan LawrenzJ Andrew McCammon
Sep 21, 2010·Journal of Molecular Modeling·Michal Raab, Igor Tvaroška
Oct 5, 2010·The Journal of Chemical Physics·Michele CeriottiDavid E Manolopoulos
Nov 26, 2010·Journal of Chemical Information and Modeling·Binh Khanh MaiMai Suan Li
May 13, 2011·Journal of the American Chemical Society·Nan-jie DengRonald M Levy
Jul 14, 2011·Nature Communications·Rommie E AmaroRobin M Bush
Jul 19, 2011·Journal of Molecular Biology·Ayşegül OzenCelia A Schiffer
Mar 3, 2012·PloS One·Kresten Lindorff-LarsenDavid E Shaw
Mar 14, 2012·PLoS Computational Biology·Cyril F ReboulAshley M Buckle
Aug 8, 2012·Proceedings of the National Academy of Sciences of the United States of America·Christian SiebenAndreas Herrmann
Sep 29, 2012·Current Pharmaceutical Design·Eric Paquet, Herna L Viktor
Nov 10, 2012·ACS Chemical Biology·Claudio PeriGiorgio Colombo
Sep 11, 2013·Biochimica Et Biophysica Acta·Raphael AlhadeffIsaiah T Arkin
Nov 5, 2013·Influenza Research and Treatment·Dimitrios VlachakisSophia Kossida

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Citations

Nov 26, 2015·Trends in Molecular Medicine·Iana H HaralambievaGregory A Poland
Feb 14, 2016·Chemical Biology & Drug Design·Mukul MahantiPär Söderhjelm
Oct 7, 2016·Interdisciplinary Sciences, Computational Life Sciences·Salman AkhtarJamal M Arif
Nov 4, 2017·Soft Matter·Xiaocheng ShangBenedict Leimkuhler
Feb 6, 2020·Annual Review of Physical Chemistry·Mehmet Ali ÖztürkRebecca C Wade
Apr 21, 2020·Journal of Biomolecular Structure & Dynamics·Jirayu KammarabutrThanyada Rungrotmongkol
Dec 8, 2017·Journal of Molecular Modeling·Anthony NashNora H de Leeuw
Nov 14, 2017·Dalton Transactions : an International Journal of Inorganic Chemistry·Fu-Qiang ZhangXian-Ming Zhang
Aug 2, 2018·Frontiers in Immunology·Kannan NatarajanDavid H Margulies
Mar 15, 2020·Physical Review. E·Niels Grønbech-Jensen, Oded Farago
Oct 10, 2020·The Journal of Chemical Physics·Joshua FinkelsteinNiels Grønbech-Jensen
Oct 23, 2020·Journal of Biomolecular Structure & Dynamics·Kanika VermaThanyada Rungrotmongkol
Mar 4, 2020·Computational and Structural Biotechnology Journal·Karolina MitusińskaArtur Góra
Feb 6, 2020·Computational and Structural Biotechnology Journal·Zhaoqian Su, Yinghao Wu
Jan 30, 2021·Biotechnology Advances·Joan Planas-IglesiasDavid Bednar
Mar 12, 2021·Chemical Reviews·Oliver T UnkeKlaus-Robert Müller
Sep 24, 2018·Physics of Life Reviews·Andrea Pérez-VillaA Marco Saitta
May 13, 2021·Chemical Reviews·Ricardo M BorgesRyan S Renslow
Jun 3, 2021·Polymers·Madjid SoltaniElham L Zoudani
Aug 14, 2020·Journal of Chemical Information and Modeling·Natesh SinghBruno O Villoutreix
Apr 3, 2020·Accounts of Chemical Research·Lur Alonso-CotchicoJean-Didier Maréchal
Aug 22, 2018·Journal of Chemical Information and Modeling·Jeffrey R WagnerRommie E Amaro

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Methods Mentioned

BETA
X-ray
nuclear magnetic resonance

Software Mentioned

CHARMM
AMBER

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