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  • Title: Membrane-associated proteins and peptides.
    Author: Lensink MF.
    Journal: Methods Mol Biol; 2008; 443():161-79. PubMed ID: 18446287.
    Abstract:
    This chapter discusses the practical aspects of setting up molecular dynamics simulations for membrane-associated proteins and peptides. Special emphasis lies on the analysis of such systems. The main focus is the association between a cationic peptide and an anionic lipid bilayer--a peptide/lipid-bilayer system--but the extension onto more complicated systems is discussed. Topology files for selected lipids and several new analysis tools relevant for protein-membrane simulations are presented, the most important ones of which are: g_helixaxis, to calculate the axis of a helix and its angle with the bilayer; g_arom, to calculate aromatic order parameters; and g_under, to calculate which lipids interact with the protein. A procedure is explained to calculate properties involving peptide-interacting lipids only, as opposed to all lipids.
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