%0 Journal Article %1 Jefferys2015Alchembed %A Jefferys, Elizabeth %A Sands, Zara A. %A Shi, Jiye %A Sansom, Mark S. P. %A Fowler, Philip W. %D 2015 %J Journal of Chemical Theory and Computation %K membrane-insertion membrane-systems molecular-dynamics %N 6 %P 2743-2754 %R 10.1021/ct501111d %T Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries %U /brokenurl# http://dx.doi.org/10.1021/ct501111d %V 11 %X 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, alchembed, 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 validate the method on a range of membrane proteins and determine the optimal soft-core parameters required to insert membrane proteins. Since all of the major biomolecular codes include soft-core van der Waals potentials, no additional code is required to apply this method. A tutorial is included in the Supporting Information.

@article{Jefferys2015Alchembed, abstract = { 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, alchembed, 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 validate the method on a range of membrane proteins and determine the optimal soft-core parameters required to insert membrane proteins. Since all of the major biomolecular codes include soft-core van der Waals potentials, no additional code is required to apply this method. A tutorial is included in the Supporting Information. }, added-at = {2016-03-15T21:18:56.000+0100}, author = {Jefferys, Elizabeth and Sands, Zara A. and Shi, Jiye and Sansom, Mark S. P. and Fowler, Philip W.}, biburl = {https://www.bibsonomy.org/bibtex/23bb497d4327cd8b05f6bfe6ddbf10232/salotz}, description = {Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries - Journal of Chemical Theory and Computation (ACS Publications)}, doi = {10.1021/ct501111d}, eprint = {http://dx.doi.org/10.1021/ct501111d}, interhash = {ec663cc79b6b32535d194b82193c407f}, intrahash = {3bb497d4327cd8b05f6bfe6ddbf10232}, journal = {Journal of Chemical Theory and Computation}, keywords = {membrane-insertion membrane-systems molecular-dynamics}, note = {PMID: 26089745}, number = 6, pages = {2743-2754}, timestamp = {2016-03-15T21:18:56.000+0100}, title = {Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries}, url = {/brokenurl# http://dx.doi.org/10.1021/ct501111d }, volume = 11, year = 2015 }