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Efficient preparation and analysis of membrane and membrane protein systems

Research output: Contribution to journalArticleScientificpeer-review

Details

Original languageEnglish
Pages (from-to)2468-2482
JournalBiochimica et Biophysica Acta: Biomembranes
Volume1858
Issue number10
Early online date4 Mar 2016
DOIs
Publication statusPublished - Oct 2016
Publication typeA1 Journal article-refereed

Abstract

Molecular dynamics (MD) simulations have become a highly important technique to consider lipid membrane systems, and quite often they provide considerable added value to laboratory experiments. Rapid development of both software and hardware has enabled the increase of time and size scales reachable by MD simulations to match those attainable by several accurate experimental techniques. However, until recently, the quality and maturity of software tools available for building membrane models for simulations as well as analyzing the results of these simulations have seriously lagged behind.Here, we discuss the recent developments of such tools from the end-users' point of view. In particular, we review the software that can be employed to build lipid bilayers and other related structures with or without embedded membrane proteins to be employed in MD simulations. Additionally, we provide a brief critical insight into force fields and MD packages commonly used for membrane and membrane protein simulations. Finally, we list analysis tools that can be used to study the properties of membrane and membrane protein systems. In all these points we comment on the respective compatibility of the covered tools.We also share our opinion on the current state of the available software. We briefly discuss the most commonly employed tools and platforms on which new software can be built. We conclude the review by providing a few ideas and guidelines on how the development of tools can be further boosted to catch up with the rapid pace at which the field of membrane simulation progresses. This includes improving the compatibility between software tools and promoting the openness of the codes on which these applications rely.This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.

ASJC Scopus subject areas

Keywords

  • Lipid bilayer, Membrane building, Molecular dynamics, Protein insertion, Tools and software

Publication forum classification

Field of science, Statistics Finland

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