Molecular dynamics simulations of membrane proteins have grown dramatically in the last 20 years. Running these simulations first requires embedding the protein’s three-dimensional structure in a lipid bilayer of a suitable composition, one that resembles its native environment. This step is far from trivial, especially for modeling heterogeneous mixtures of lipids. CHARMM-GUI, a webserver for simulation system preparation greatly simplifies this step, allowing for the construction of complex heterogeneous and/or asymmetric membranes. Here, we demonstrate how to use CHARMM-GUI to build the membrane for the outer-membrane protein BamA.
CITATION STYLE
Li, Y., Liu, J., & Gumbart, J. C. (2021). Preparing Membrane Proteins for Simulation Using CHARMM-GUI. In Methods in Molecular Biology (Vol. 2302, pp. 237–251). Humana Press Inc. https://doi.org/10.1007/978-1-0716-1394-8_13
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