Article

Fly-casting with ligand–sliding and orientational selection to support the complex formation of a GPCR and a middle-sized flexible molecule

2022-03-02

Abstract excerpt

To elucidate computationally a binding mechanism of a middle-sized flexible molecule, bosentan, to a GPCR protein, human endothelin receptor type B (hETB), a GA-guided multidimensional virtual-system coupled molecular dynamics (GA-mD-VcMD) simulation was performed. This method is one of generalized ensemble methods and produces a free-energy landscape of the ligand-receptor binding by searching large-scale motions...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 3ad70cbe-c769-5429-b8b0-83a67745ba71
DOI: 10.1101/2022.02.28.482421

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Fly-casting with ligand–sliding and orientational selection to support the complex formation of a GPCR and a middle-sized flexible moleculeDOI 10.1101/2022.02.28.482421Read

Fly-Casting with Ligand–Sliding and Orientational Selection to Support the Complex Formation of a GPCR and a Middle-Sized Flexible MoleculeSemantic proximity Read

Hot-Spot Residues to be Mutated Common in G Protein-Coupled Receptors of Class A: Identification of Thermostabilizing Mutations Followed by Determination of Three-Dimensional Structures for Two Example Receptors.Semantic proximity Read

Substrate Transport is Mediated not only by P-glycoprotein but also by Lipid PenetrationSemantic proximity Read

Deep Learning Dynamic Allostery of G-Protein-Coupled ReceptorsSemantic proximity Read

SuperBiHelix method for predicting the pleiotropic ensemble of G-protein-coupled receptor conformations.Semantic proximity Read

Probing Allosteric Regulation Mechanism of W7.35 on Agonist-Induced Activity for μOR by Mutation Simulation.Semantic proximity Read

Toward an evolutionary containment of evolving pathogen-receptors by using an ensemble of multiple mutant ligands: from the viewpoint of fitness landscape in sequence space.Semantic proximity Read

Conformational ensemble view of G protein-coupled receptors and the effect of mutations and ligand binding.Semantic proximity Read

The switch states of the GDP-bound HRAS affected by point mutations: a study from Gaussian accelerated molecular dynamics simulations and free energy landscapes.Semantic proximity Read

Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics.Semantic proximity Read

A Dynamic Picture of the Early Events in Nociceptin Binding to the NOP Receptor by Metadynamics.Semantic proximity Read