Literature DB >> 26766518

Force Field Development for Lipid Membrane Simulations.

Alexander P Lyubartsev1, Alexander L Rabinovich2.   

Abstract

With the rapid development of computer power and wide availability of modelling software computer simulations of realistic models of lipid membranes, including their interactions with various molecular species, polypeptides and membrane proteins have become feasible for many research groups. The crucial issue of the reliability of such simulations is the quality of the force field, and many efforts, especially in the latest several years, have been devoted to parametrization and optimization of the force fields for biomembrane modelling. In this review, we give account of the recent development in this area, covering different classes of force fields, principles of the force field parametrization, comparison of the force fields, and their experimental validation. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
Copyright © 2016. Published by Elsevier B.V.

Entities:  

Keywords:  Biomembranes; Force fields; Lipid bilayers; Molecular dynamics

Mesh:

Substances:

Year:  2016        PMID: 26766518     DOI: 10.1016/j.bbamem.2015.12.033

Source DB:  PubMed          Journal:  Biochim Biophys Acta        ISSN: 0006-3002


  25 in total

1.  Structural Behavior of the Peptaibol Harzianin HK VI in a DMPC Bilayer: Insights from MD Simulations.

Authors:  Marina Putzu; Sezgin Kara; Sergii Afonin; Stephan L Grage; Andrea Bordessa; Grégory Chaume; Thierry Brigaud; Anne S Ulrich; Tomáš Kubař
Journal:  Biophys J       Date:  2017-06-20       Impact factor: 4.033

2.  Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance.

Authors:  Giray Enkavi; Matti Javanainen; Waldemar Kulig; Tomasz Róg; Ilpo Vattulainen
Journal:  Chem Rev       Date:  2019-03-12       Impact factor: 60.622

3.  Challenges and advances in atomistic simulations of potassium and sodium ion channel gating and permeation.

Authors:  Kevin R DeMarco; Slava Bekker; Igor Vorobyov
Journal:  J Physiol       Date:  2018-12-19       Impact factor: 5.182

4.  Electropore Formation in Mechanically Constrained Phospholipid Bilayers.

Authors:  M Laura Fernández; Marcelo Raúl Risk; P Thomas Vernier
Journal:  J Membr Biol       Date:  2017-11-23       Impact factor: 1.843

5.  Computer simulations of protein-membrane systems.

Authors:  Jennifer Loschwitz; Olujide O Olubiyi; Jochen S Hub; Birgit Strodel; Chetan S Poojari
Journal:  Prog Mol Biol Transl Sci       Date:  2020-02-26       Impact factor: 3.622

6.  Lipid molecules can induce an opening of membrane-facing tunnels in cytochrome P450 1A2.

Authors:  Petr Jeřábek; Jan Florián; Václav Martínek
Journal:  Phys Chem Chem Phys       Date:  2016-11-09       Impact factor: 3.676

7.  Accelerating Membrane Simulations with Hydrogen Mass Repartitioning.

Authors:  Curtis Balusek; Hyea Hwang; Chun Hon Lau; Karl Lundquist; Anthony Hazel; Anna Pavlova; Diane L Lynch; Patricia H Reggio; Yi Wang; James C Gumbart
Journal:  J Chem Theory Comput       Date:  2019-07-02       Impact factor: 6.006

8.  Simulation Best Practices for Lipid Membranes [Article v1.0].

Authors:  David J Smith; Jeffery B Klauda; Alexander J Sodt
Journal:  Living J Comput Mol Sci       Date:  2019-01-09

Review 9.  Dynamic pattern generation in cell membranes: Current insights into membrane organization.

Authors:  Krishnan Raghunathan; Anne K Kenworthy
Journal:  Biochim Biophys Acta Biomembr       Date:  2018-05-09       Impact factor: 3.747

Review 10.  Microscopic view of lipids and their diverse biological functions.

Authors:  Po-Chao Wen; Paween Mahinthichaichan; Noah Trebesch; Tao Jiang; Zhiyu Zhao; Eric Shinn; Yuhang Wang; Mrinal Shekhar; Karan Kapoor; Chun Kit Chan; Emad Tajkhorshid
Journal:  Curr Opin Struct Biol       Date:  2018-07-23       Impact factor: 6.809

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