Automated builder and database of protein/membrane complexes for molecular dynamics simulations.

ABSTRACT: Molecular dynamics simulations of membrane proteins have provided deeper insights into their functions and interactions with surrounding environments at the atomic level. However, compared to solvation of globular proteins, building a realistic protein/membrane complex is still challenging and requires considerable experience with simulation software. Membrane Builder in the CHARMM-GUI website (http://www.charmm-gui.org) helps users to build such a complex system using a web browser with a graphical user interface. Through a generalized and automated building process including system size determination as well as generation of lipid bilayer, pore water, bulk water, and ions, a realistic membrane system with virtually any kinds and shapes of membrane proteins can be generated in 5 minutes t

SUBMITTER: Jo S 

PROVIDER: S-EPMC1963319 | biostudies-literature | 2007 Sep

REPOSITORIES: biostudies-literature