Statistics for the analysis of molecular dynamics simulations: providing P values for agonist-dependent GPCR activation.

ABSTRACT: Molecular dynamics (MD) is the common computational technique for assessing efficacy of GPCR-bound ligands. Agonist efficacy measures the capability of the ligand-bound receptor of reaching the active state in comparison with the free receptor. In this respect, agonists, neutral antagonists and inverse agonists can be considered. A collection of MD simulations of both the ligand-bound and the free receptor are needed to provide reliable conclusions. Variability in the trajectories needs quantification and proper statistical tools for meaningful and non-subjective conclusions. Multiple-factor (time, ligand, lipid) ANOVA with repeated measurements on the time factor is proposed as a suitable statistical method for the analysis of agonist-dependent GPCR activation MD simulations. Inclusion of

SUBMITTER: Bruzzese A 

PROVIDER: S-EPMC7672096 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature