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ABSTRACT:
SUBMITTER: Jefferys E
PROVIDER: S-EPMC4467903 | biostudies-literature | 2015 Jun
REPOSITORIES: biostudies-literature
Jefferys Elizabeth E Sands Zara A ZA Shi Jiye J Sansom Mark S P MS Fowler Philip W PW
Journal of chemical theory and computation 20150514 6
A necessary step prior to starting any membrane protein computer simulation is the creation of a well-packed configuration of protein(s) and lipids. Here, we demonstrate a method, <i>alchembed</i>, that can simultaneously and rapidly embed multiple proteins into arrangements of lipids described using either atomistic or coarse-grained force fields. During a short simulation, the interactions between the protein(s) and lipids are gradually switched on using a soft-core van der Waals potential. We ...[more]