LipIDens: simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins.

ABSTRACT: Cryo-electron microscopy (cryo-EM) enables the determination of membrane protein structures in native-like environments. Characterising how membrane proteins interact with the surrounding membrane lipid environment is assisted by resolution of lipid-like densities visible in cryo-EM maps. Nevertheless, establishing the molecular identity of putative lipid and/or detergent densities remains challenging. Here we present LipIDens, a pipeline for molecular dynamics (MD) simulation-assisted interpretation of lipid and lipid-like densities in cryo-EM structures. The pipeline integrates the implementation and analysis of multi-scale MD simulations for identification, ranking and refinement of lipid binding poses which superpose onto cryo-EM map densities. Thus, LipIDens enables direct integration

SUBMITTER: Ansell TB 

PROVIDER: S-EPMC10682427 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature