MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes.

摘要: There has been exponential growth in the number of membrane protein structures determined. Nevertheless, these are usually resolved absence their lipid environment. Coarse-grained molecular dynamics (CGMD) simulations enable insertion proteins into explicit models bilayers. We have automated CGMD methodology, enabling to be identified upon release PDB and embedded a membrane. The analyzed for protein-lipid interactions, identifying binding sites, revealing local bilayer deformations plus access pathways within coarse-grained protein/bilayer complexes transformed atomistic resolution further analysis simulation. Using this simulation pipeline, we recently determined predict locations membrane, lipid/protein functional implications an enhanced understanding environment each protein.