Accelerated Molecular Dynamics Simulations | List of Frontiers open access articles

Brief Research Report

Published on 30 Oct 2019

Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations

in Biological Modeling and Simulation

Jinan Wang
Andrey Alekseenko
Dima Kozakov
Yinglong Miao

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2019.00112

24,965 views
91 citations

Original Research

Published on 15 Nov 2021

An Unbound Proline-Rich Signaling Peptide Frequently Samples Cis Conformations in Gaussian Accelerated Molecular Dynamics Simulations

in Molecular Recognition

Juan Alcantara
Robyn Stix
Katherine Huang
Acadia Connor
Ray East
Valeria Jaramillo-Martinez
Elliott J. Stollar
K. Aurelia Ball

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2021.734169

8,223 views
16 citations

Original Research

Published on 17 Dec 2019

Conformation Transition of Intracellular Part of Glucagon Receptor in Complex With Agonist Glucagon by Conventional and Accelerated Molecular Dynamics Simulations

in Medicinal and Pharmaceutical Chemistry

Qifeng Bai
Shuoyan Tan
Horacio Pérez-Sánchez
Haixia Feng
Liya Feng
HuanXiang Liu
Xiaojun Yao

Frontiers in Chemistry

doi 10.3389/fchem.2019.00851

4,144 views
9 citations

Original Research

Published on 23 Jan 2023

Elucidating the molecular determinants in the process of gastrin C-terminal pentapeptide amide end activating cholecystokinin 2 receptor by Gaussian accelerated molecular dynamics simulations

in Gastrointestinal and Hepatic Pharmacology

Kecheng Yang
Huiyuan Jin
Xu Gao
Gang-Cheng Wang
Guo-Qiang Zhang

Frontiers in Pharmacology

doi 10.3389/fphar.2022.1054575

3,210 views
3 citations

Original Research

Published on 26 Feb 2021

Conformational Changes of Glutamine 5′-Phosphoribosylpyrophosphate Amidotransferase for Two Substrates Analogue Binding: Insight from Conventional Molecular Dynamics and Accelerated Molecular Dynamics Simulations

in Theoretical and Computational Chemistry

Congcong Li
Siao Chen
Tianci Huang
Fangning Zhang
Jiawei Yuan
Hao Chang
Wannan Li
Weiwei Han

Frontiers in Chemistry

doi 10.3389/fchem.2021.640994

5,079 views
9 citations

Original Research

Published on 13 Aug 2024

Computational insights into the mechanisms underlying structural destabilization and recovery in trafficking-deficient hERG mutants

in Biological Modeling and Simulation

Sara AlRawashdeh
Farag E. S. Mosa
Khaled H. Barakat

Frontiers in Molecular Biosciences

doi 10.3389/fmolb.2024.1341727

2,757 views

Articles

Improved Modeling of Peptide-Protein Binding Through Global Docking and Accelerated Molecular Dynamics Simulations

An Unbound Proline-Rich Signaling Peptide Frequently Samples Cis Conformations in Gaussian Accelerated Molecular Dynamics Simulations

Conformation Transition of Intracellular Part of Glucagon Receptor in Complex With Agonist Glucagon by Conventional and Accelerated Molecular Dynamics Simulations

Elucidating the molecular determinants in the process of gastrin C-terminal pentapeptide amide end activating cholecystokinin 2 receptor by Gaussian accelerated molecular dynamics simulations

Conformational Changes of Glutamine 5′-Phosphoribosylpyrophosphate Amidotransferase for Two Substrates Analogue Binding: Insight from Conventional Molecular Dynamics and Accelerated Molecular Dynamics Simulations

Computational insights into the mechanisms underlying structural destabilization and recovery in trafficking-deficient hERG mutants