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MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
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2014 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1460-2059, Vol. 30, no 3, 439-441 p.Article in journal (Refereed) Published
Abstract [en]

Motivation: Molecular dynamics (MD) simulations have had a profound impact on studies of membrane proteins during past two decades, but the accuracy of MD simulations of membranes is limited by the quality of membrane models and the applied force fields. Membrane models used in MD simulations mostly contain one kind of lipid molecule. This is far from reality, for biological membranes always contain more than one kind of lipid molecule. Moreover, the lipid composition and their distribution are functionally important. As a result, there is a necessity to prepare more realistic lipid membranes containing different types of lipids at physiological concentrations. Results: To automate and simplify the building process of heterogeneous lipid bilayers as well as providing molecular topologies for included lipids based on both united and all-atom force fields, we provided MemBuilder as a web-based graphical user interface.

Place, publisher, year, edition, pages
2014. Vol. 30, no 3, 439-441 p.
National Category
Natural Sciences
URN: urn:nbn:se:uu:diva-220998DOI: 10.1093/bioinformatics/btt680ISI: 000331271100022OAI: oai:DiVA.org:uu-220998DiVA: diva2:707613
Available from: 2014-03-25 Created: 2014-03-24 Last updated: 2014-03-25Bibliographically approved

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Zhang, Jinvan der Spoel, David
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