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Molecular dynamics simulations have become a popular and powerful technique to study lipids and membrane proteins. We present some general questions and issues that should be considered prior to embarking on molecular dynamics simulation studies of membrane proteins and review common simulation methods. We suggest a practical approach to setting up and running simulations of membrane proteins, and...
Computer simulations are rapidly becoming a standard tool to study the structure and dynamics of lipids and membrane proteins. Increasing computer capacity allows unbiased simulations of lipid and membrane-active peptides. With the increasing number of high-resolution structures of membrane proteins, which also enables homology modelling of more structures, a wide range of membrane proteins can now...
The forces contributing to the association of transmembrane helices in folded membrane proteins have received considerable attention recently. In this study we investigate the importance of hydrogen bonding by studying the effect of a single Asn residue in the center of an otherwise hydrophobic transmembrane peptide using computer simulations. We use the model peptide MS1 which has been derived from...
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