Recent advances and applications of molecular docking to G protein-coupled receptors

D Bartuzi, AA Kaczor, KM Targowska-Duda… - Molecules, 2017 - mdpi.com
The growing number of studies on G protein-coupled receptors (GPCRs) family are a source
of noticeable improvement in our understanding of the functioning of these proteins. GPCRs …

Property-unmatched decoys in docking benchmarks

RM Stein, Y Yang, TE Balius, MJ O'Meara… - Journal of chemical …, 2021 - ACS Publications
Enrichment of ligands versus property-matched decoys is widely used to test and optimize
docking library screens. However, the unconstrained optimization of enrichment alone can …

In silico ligand docking approaches to characterise the binding of known allosteric modulators to the glucagon-like peptide 1 receptor and prediction of ADME/Tox …

CS Odoemelam, E Hunter, J Simms, Z Ahmad… - Applied …, 2022 - mdpi.com
The glucagon-like peptide 1 receptor (GLP-1R) is a member of the family (or class) B G-
protein-coupled receptor (GPCR). The receptor is a regulator of insulin and a key target in …

Continuous evaluation of ligand protein predictions: a weekly community challenge for drug docking

JR Wagner, CP Churas, S Liu, RV Swift, M Chiu… - Structure, 2019 - cell.com
Docking calculations can accelerate drug discovery by predicting the bound poses of
ligands for a targeted protein. However, it is not clear which docking methods work best …

Virtual screening of human class-a GPCRs using ligand profiles built on multiple ligand–receptor interactions

WKB Chan, Y Zhang - Journal of molecular biology, 2020 - Elsevier
G protein-coupled receptors (GPCRs) are a large family of integral membrane proteins
responsible for cellular signal transductions. Identification of therapeutic compounds to …

Sequential ligand-and structure-based virtual screening approach for the identification of potential G protein-coupled estrogen receptor-1 (GPER-1) modulators

SU Khan, N Ahemad, LH Chuah, R Naidu, TT Htar - RSC advances, 2019 - pubs.rsc.org
G protein-coupled estrogen receptor-1 (GPER-1) is a seven transmembrane receptor,
responsible for mediating rapid estrogen signaling in many physiological responses in …

[HTML][HTML] A membrane protein complex docking benchmark

PI Koukos, I Faro, CW van Noort… - Journal of molecular …, 2018 - Elsevier
We report the first membrane protein–protein docking benchmark consisting of 37 targets of
diverse functions and folds. The structures were chosen based on a set of parameters such …

Discovery of non-peptide GLP-1r natural agonists for enhancing coronary safety in type 2 diabetes patients

N Shakour, S Hoseinpoor, F Rajabian… - Journal of …, 2023 - Taylor & Francis
This study explores the computational discovery of non-peptide agonists targeting the
Glucagon-Like Peptide-1 Receptor (GLP-1R) to enhance the safety of major coronary …

Kinase-Bench: Comprehensive Benchmarking Tools and Guidance for Achieving Selectivity in Kinase Drug Discovery

TH Wei, SS Zhou, XL Jing, JC Liu, M Sun… - Journal of Chemical …, 2024 - ACS Publications
Developing selective kinase inhibitors remains a formidable challenge in drug discovery
because of the highly conserved structural information on adenosine triphosphate (ATP) …

Application of GPCR structures for modelling of free fatty acid receptors

IG Tikhonova - Free Fatty Acid Receptors, 2017 - Springer
Five G protein-coupled receptors (GPCRs) have been identified to be activated by free fatty
acids (FFA). Among them, FFA1 (GPR40) and FFA4 (GPR120) bind long-chain fatty acids …