Understanding the microscopic binding mechanism of hydroxylated and sulfated polybrominated diphenyl ethers with transthyretin by molecular docking, molecular dynamics simulations and binding free energy calculations

Binding Mechanism ◽

Diphenyl Ethers ◽

Dynamics Simulations

The binding of TTR with sulfated-PBDEs and OH-PBDEs shows different molecular recognition mechanisms.

Prediction of the Binding Affinities and Selectivity for CB1 and CB2 Ligands Using Homology Modeling, Molecular Docking, Molecular Dynamics Simulations, and MM-PBSA Binding Free Energy Calculations

ACS Chemical Neuroscience ◽

10.1021/acschemneuro.9b00696 ◽

2020 ◽

Vol 11 (8) ◽

pp. 1139-1158 ◽

Cited By ~ 3

Author(s):

Beihong Ji ◽

Shuhan Liu ◽

Xibing He ◽

Viet Hoang Man ◽

Xiang-Qun Xie ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Docking ◽

Homology Modeling ◽

Binding Free Energy ◽

Binding Affinities ◽

Dynamics Simulations

Probing the “fingers” domain binding pocket of Hepatitis C virus NS5B RdRp and D559G resistance mutation via molecular docking, molecular dynamics simulation and binding free energy calculations

10.1080/07391102.2018.1491419 ◽

2018 ◽

Vol 37 (9) ◽

pp. 2440-2456 ◽

Cited By ~ 4

Author(s):

Saravanan Manjula ◽

Magudeeswaran Sivanandam ◽

Poomani Kumaradhas

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Docking ◽

Hepatitis C ◽

Binding Free Energy ◽

Resistance Mutation ◽

Binding Pocket ◽

Dynamics Simulation ◽

Binding Free Energy Calculations

Investigation of intermolecular interactions and binding mechanism of PU139 and PU141 molecules with p300 HAT enzyme via molecular docking, molecular dynamics simulations and binding free energy analysis

10.1080/07391102.2021.2020164 ◽

2022 ◽

pp. 1-15

Author(s):

Jaganathan Ramakrishnan ◽

Sivanandam Magudeeswaran ◽

Suganya Suresh ◽

Kumaradhas Poomani

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Docking ◽

Intermolecular Interactions ◽

Energy Analysis ◽

Binding Free Energy ◽

Binding Mechanism ◽

Dynamics Simulations ◽

Free Energy Analysis

Computational investigation of the HIV-1 Rev multimerization using molecular dynamics simulations and binding free energy calculations

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.24057 ◽

2012 ◽

Vol 80 (6) ◽

pp. 1633-1646 ◽

Cited By ~ 6

Author(s):

Tom Venken ◽

Dirk Daelemans ◽

Marc De Maeyer ◽

Arnout Voet

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Computational Investigation ◽

Energy Calculations ◽

Dynamics Simulations ◽

Hiv 1

Revealing binding selectivity of ligands toward murine double minute 2 and murine double minute X based on molecular dynamics simulations and binding free energy calculations

10.1080/07391102.2019.1695671 ◽

2019 ◽

Vol 38 (17) ◽

pp. 5081-5094 ◽

Cited By ~ 1

Author(s):

Shuhua Shi ◽

Kai Sui ◽

Weizhe Liu ◽

Yanzi Lei ◽

Shaolong Zhang ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Energy Calculations ◽

Double Minute ◽

Murine Double Minute ◽

Dynamics Simulations

Absolute Binding Free Energy Calculations Using Molecular Dynamics Simulations with Restraining Potentials

Biophysical Journal ◽

10.1529/biophysj.106.084301 ◽

2006 ◽

Vol 91 (8) ◽

pp. 2798-2814 ◽

Cited By ~ 234

Author(s):

Jiyao Wang ◽

Yuqing Deng ◽

Benoît Roux

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Energy Calculations ◽

Dynamics Simulations ◽

Absolute Binding Free Energy

Investigation on the binding mechanism of loratinib with the c-ros oncogene 1 (ROS1) receptor tyrosine kinase via molecular dynamics simulation and binding free energy calculations

10.1080/07391102.2017.1378127 ◽

2017 ◽

Vol 36 (12) ◽

pp. 3106-3113 ◽

Cited By ~ 4

Author(s):

Xiaoyun Wu ◽

Yuanyuan Wang ◽

Shanhe Wan ◽

Jiajie Zhang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Tyrosine Kinase ◽

Receptor Tyrosine Kinase ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Binding Mechanism ◽

Binding Free Energy Calculations

Faculty Opinions recommendation of Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1047901.497924 ◽

2006 ◽

Author(s):

Jeffry Madura

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Energy Calculations ◽

Dynamics Simulations ◽

Absolute Binding Free Energy

Insight into herbicide resistance of W574L mutant Arabidopsis thaliana acetohydroxyacid synthase: molecular dynamics simulations and binding free energy calculations

Science China Chemistry ◽

10.1007/s11426-010-0024-0 ◽

2010 ◽

Vol 53 (1) ◽

pp. 91-102 ◽

Cited By ~ 8

Author(s):

ZhiHong Yu ◽

Xin Wen ◽

Zhen Xi

Keyword(s):

Molecular Dynamics ◽

Arabidopsis Thaliana ◽

Free Energy ◽

Herbicide Resistance ◽

Binding Free Energy ◽

Acetohydroxyacid Synthase ◽

Dynamics Simulations ◽

Insight Into

Interaction between gp120 and ligand in HIV-1 env protein: Molecular dynamics simulations and binding free energy calculations

10.1063/1.5122491 ◽

2019 ◽

Author(s):

Vishnudatt Pandey ◽

Gargi Tiwari ◽

Vijaya Shri Mall ◽

Rakesh Kumar Tiwari ◽

Rajendra Prasad Ojha

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Binding Free Energy ◽

Env Protein ◽

Dynamics Simulations ◽

Protein Molecular Dynamics ◽

Hiv 1