The binding mechanism of a novel nicotinamide isostere inhibiting with TNKSs: a molecular dynamic simulation and binding free energy calculation

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2015.1043580 ◽

2015 ◽

Vol 34 (3) ◽

pp. 517-528 ◽

Author(s):

Ting-Ting Feng ◽

Yan-Jun Zhang ◽

H. Chen ◽

Song Fan ◽

Ju-Guang Han

Keyword(s):

Free Energy ◽

Molecular Dynamic Simulation ◽

Molecular Dynamic ◽

Dynamic Simulation ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Binding Mechanism ◽

Binding Free Energy Calculation

Download Full-text

Investigation of the interactions between Melittin and the PLGA and PLA polymers: molecular dynamic simulation and binding free energy calculation

Materials Research Express ◽

10.1088/2053-1591/ab06d3 ◽

2019 ◽

Vol 6 (5) ◽

pp. 055318 ◽

Author(s):

Homayoun Asadzadeh ◽

Ali Moosavi

Keyword(s):

Free Energy ◽

Molecular Dynamic Simulation ◽

Molecular Dynamic ◽

Dynamic Simulation ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Binding Free Energy Calculation

Download Full-text

Evaluation of Interactions between Urokinase Plasminogen and Inhibitors Using Molecular Dynamic Simulation and Free-Energy Calculation

The Journal of Physical Chemistry A ◽

10.1021/jp5064319 ◽

2014 ◽

Vol 118 (39) ◽

pp. 9113-9119 ◽

Author(s):

Rongjian Sa ◽

Liang Fang ◽

Mingdong Huang ◽

Qiaohong Li ◽

Yongqin Wei ◽

...

Keyword(s):

Free Energy ◽

Molecular Dynamic Simulation ◽

Molecular Dynamic ◽

Dynamic Simulation ◽

Free Energy Calculation ◽

Energy Calculation

Download Full-text

Computational identification of 2,4-disubstituted amino-pyrimidines as L858R/T790M-EGFR double mutant inhibitors using pharmacophore mapping, molecular docking, binding free energy calculation, DFT study and molecular dynamic simulation

In Silico Pharmacology ◽

10.1007/s40203-021-00113-x ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Rahul Pawara ◽

Iqrar Ahmad ◽

Sanjay Surana ◽

Harun Patel

Keyword(s):

Free Energy ◽

Molecular Docking ◽

Molecular Dynamic Simulation ◽

Dynamic Simulation ◽

Double Mutant ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Pharmacophore Mapping ◽

Computational Identification

Download Full-text

Investigation on the mechanism for the binding and drug resistance of wild type and mutations of G86 residue in HIV-1 protease complexed with Darunavir by molecular dynamic simulation and free energy calculation

Journal of Molecular Modeling ◽

10.1007/s00894-014-2122-y ◽

2014 ◽

Vol 20 (2) ◽

Author(s):

Dan Li ◽

Ying Zhang ◽

Run-Ning Zhao ◽

Song Fan ◽

Ju-Guang Han

Keyword(s):

Drug Resistance ◽

Free Energy ◽

Molecular Dynamic Simulation ◽

Molecular Dynamic ◽

Dynamic Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Wild Type ◽

Download Full-text

Insights into drug resistance of mutations D30N and I50V to HIV-1 protease inhibitor TMC-114: Free energy calculation and molecular dynamic simulation

Journal of Molecular Modeling ◽

10.1007/s00894-009-0553-7 ◽

2009 ◽

Vol 16 (3) ◽

pp. 459-468 ◽

Author(s):

Jianzhong Chen ◽

Shaolong Zhang ◽

Xinguo Liu ◽

Qinggang Zhang

Keyword(s):

Drug Resistance ◽

Free Energy ◽

Protease Inhibitor ◽

Molecular Dynamic Simulation ◽

Molecular Dynamic ◽

Dynamic Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Download Full-text

Binding free energy calculation of human beta defensin 3 with negatively charged lipid bilayer using free energy perturbation method

Biophysical Chemistry ◽

10.1016/j.bpc.2021.106662 ◽

2021 ◽

pp. 106662

Author(s):

Ann Brewer ◽

Liqun Zhang

Keyword(s):

Free Energy ◽

Perturbation Method ◽

Lipid Bilayer ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Free Energy Perturbation ◽

Energy Calculation ◽

Binding Free Energy Calculation ◽

Energy Perturbation

Download Full-text

Investigation on the characteristics and mechanisms of ACE inhibitory peptides by a thorough analysis of all 8000 tripeptides via binding free energy calculation

Food Science & Nutrition ◽

10.1002/fsn3.2253 ◽

2021 ◽

Author(s):

Ruiyao Chen ◽

Yulu Miao ◽

Xuan Hao ◽

Bei Gao ◽

Mingzhe Ma ◽

...

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Inhibitory Peptides ◽

Binding Free Energy Calculation ◽

Ace Inhibitory Peptides ◽

Download Full-text

Protein-Protein Interactions: Interface Analysis, Binding Free Energy Calculation and Interaction Design

Acta Physico-Chimica Sinica ◽

10.3866/pku.whxb20100725 ◽

2010 ◽

Vol 26 (07) ◽

pp. 1988-1997

Author(s):

BAI Hong-Jun ◽

◽

◽

LAI Lu-Hua ◽

◽

...

Keyword(s):

Free Energy ◽

Protein Interactions ◽

Interaction Design ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Protein Protein Interactions ◽

Interface Analysis ◽

Binding Free Energy Calculation

Download Full-text

Binding Free Energy Calculation of Protein-Carbohydrate Complexes: Learnings so Far

Biophysical Journal ◽

10.1016/j.bpj.2017.11.365 ◽

2018 ◽

Vol 114 (3) ◽

pp. 57a

Author(s):

Sushil K. Mishra ◽

Jaroslav Koča ◽

Yoshiki Yamaguchi

Keyword(s):

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Binding Free Energy Calculation

Download Full-text

Insights into the mechanism of inhibition of phospholipase A2 by resveratrol: An extensive molecular dynamics simulation and binding free energy calculation

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2020.107649 ◽

2020 ◽

Vol 100 ◽

pp. 107649

Author(s):

Sajedeh Sharifpour ◽

Sara Fakhraee ◽

Reza Behjatmanesh-Ardakani

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Phospholipase A2 ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Binding Free Energy Calculation ◽

Mechanism Of Inhibition

Download Full-text