COGRIMEN: Coarse-Grained Method for Modeling of Membrane Proteins in Implicit Environments.

ABSTRACT: The presented methodology is based on coarse-grained representation of biomolecules in implicit environments and is designed for the molecular dynamics simulations of membrane proteins and their complexes. The membrane proteins are not only found in the cell membrane but also in all membranous compartments of the cell: Golgi apparatus, mitochondria, endosomes and lysosomes, and they usually form large complexes. To investigate such systems the methodology is proposed based on two independent approaches combining the coarse-grained MARTINI model for proteins and the effective energy function to mimic the water/membrane environments. The latter is based on the implicit environment developed for all-atom simulations in the IMM1 method. The force field solvation parameters for COGRIMEN were in

SUBMITTER: Miszta P 

PROVIDER: S-EPMC9476660 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature