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LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry

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  • Jacob D Durrant
  • Rommie E Amaro

Abstract

As ever larger and more complex biological systems are modeled in silico, approximating physiological lipid bilayers with simple planar models becomes increasingly unrealistic. In order to build accurate large-scale models of subcellular environments, models of lipid membranes with carefully considered, biologically relevant curvature will be essential. In the current work, we present a multi-scale utility called LipidWrapper capable of creating curved membrane models with geometries derived from various sources, both experimental and theoretical. To demonstrate its utility, we use LipidWrapper to examine an important mechanism of influenza virulence. A copy of the program can be downloaded free of charge under the terms of the open-source FreeBSD License from http://nbcr.ucsd.edu/lipidwrapper. LipidWrapper has been tested on all major computer operating systems.

Suggested Citation

  • Jacob D Durrant & Rommie E Amaro, 2014. "LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry," PLOS Computational Biology, Public Library of Science, vol. 10(7), pages 1-11, July.
    • Handle: RePEc:plo:pcbi00:1003720
    DOI: 10.1371/journal.pcbi.1003720
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    1. Gongpu Zhao & Juan R. Perilla & Ernest L. Yufenyuy & Xin Meng & Bo Chen & Jiying Ning & Jinwoo Ahn & Angela M. Gronenborn & Klaus Schulten & Christopher Aiken & Peijun Zhang, 2013. "Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics," Nature, Nature, vol. 497(7451), pages 643-646, May.
    2. Andreas M. Anger & Jean-Paul Armache & Otto Berninghausen & Michael Habeck & Marion Subklewe & Daniel N. Wilson & Roland Beckmann, 2013. "Structures of the human and Drosophila 80S ribosome," Nature, Nature, vol. 497(7447), pages 80-85, May.
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    1. Yu-Xi Tsai & Yu-Chun Chien & Min-Feng Hsu & Kay-Hooi Khoo & Shang-Te Danny Hsu, 2025. "Molecular basis of host recognition of human coronavirus 229E," Nature Communications, Nature, vol. 16(1), pages 1-15, December.

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