Počet záznamů: 1
Efficient preparation and analysis of membrane and membrane protein systems
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SYSNO ASEP 0463890 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název Efficient preparation and analysis of membrane and membrane protein systems Tvůrce(i) Javanainen, M. (FI)
Martinez-Seara, Hector (UOCHB-X) RID, ORCIDZdroj.dok. Biochimica Et Biophysica Acta-Biomembranes. - : Elsevier - ISSN 0005-2736
Roč. 1858, č. 10 (2016), s. 2468-2482Poč.str. 15 s. Jazyk dok. eng - angličtina Země vyd. NL - Nizozemsko Klíč. slova tools and software ; membrane building ; protein insertion ; molecular dynamics ; lipid bilayer Vědní obor RIV CF - Fyzikální chemie a teoretická chemie Institucionální podpora UOCHB-X - RVO:61388963 UT WOS 000382340100018 EID SCOPUS 84959908239 DOI 10.1016/j.bbamem.2016.02.036 Anotace 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. Pracoviště Ústav organické chemie a biochemie Kontakt asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Viktorie Chládková, Tel.: 232 002 434 Rok sběru 2017
Počet záznamů: 1