Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs.

07:00 EST 1st January 2019 | BioPortfolio

Summary of "Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs."

Rhodopsin is a light-driven G protein-coupled receptor mediating signal transduction in eyes. The molecular dynamics (MD) simulations are powerful computational tools to investigate molecular behavior of proteins and internal water molecules which are related to the function of proteins; however, the MD simulations of the rhodopsin require several technical setups for accurate calculations. This chapter discusses practical methods for setting up the MD simulations of the rhodopsin [preparation of initial systems, condition files for MD simulation package GROMACS, and data analysis]. The data analysis includes the root mean square deviation (RMSD) and mapping of accessibility of water molecules.


Journal Details

This article was published in the following journal.

Name: Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Pages: 21-30


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