Benchmarking GPCR homology model template selection in combination with de novo loop generation.

ABSTRACT: G protein-coupled receptors (GPCR) comprise the largest family of membrane proteins and are of considerable interest as targets for drug development. However, many GPCR structures remain unsolved. To address the structural ambiguity of these receptors, computational tools such as homology modeling and loop modeling are often employed to generate predictive receptor structures. Here we combined both methods to benchmark a protocol incorporating homology modeling based on a locally selected template and extracellular loop modeling that additionally evaluates the presence of template ligands during these modeling steps. Ligands were also docked using three docking methods and two pose selection methods to elucidate an optimal ligand pose selection method. Results suggest that local template-b

SUBMITTER: Szwabowski GL 

PROVIDER: S-EPMC7484324 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature