Induced fit docking, free energy calculation and molecular dynamics studies on Mycobacterium tuberculosis alanine racemase inhibitor

Mohammed Afzal Azam; Unni Jayaram

doi:10.1080/08927022.2017.1393811

Induced fit docking, free energy calculation and molecular dynamics studies on Mycobacterium tuberculosis alanine racemase inhibitor

Molecular Simulation ◽

10.1080/08927022.2017.1393811 ◽

2017 ◽

Vol 44 (5) ◽

pp. 424-432 ◽

Cited By ~ 1

Author(s):

Mohammed Afzal Azam ◽

Unni Jayaram

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Mycobacterium Tuberculosis ◽

Free Energy Calculation ◽

Alanine Racemase ◽

Energy Calculation ◽

Induced Fit Docking ◽

Induced Fit

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An explorative study on Staphylococcus aureus MurE inhibitor: induced fit docking, binding free energy calculation, and molecular dynamics

Journal of Receptors and Signal Transduction ◽

10.1080/10799893.2019.1605528 ◽

2019 ◽

Vol 39 (1) ◽

pp. 45-54 ◽

Cited By ~ 1

Author(s):

Mohammed Afzal Azam ◽

Niladri Saha ◽

Srikanth Jupudi

Keyword(s):

Molecular Dynamics ◽

Staphylococcus Aureus ◽

Free Energy ◽

Binding Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Induced Fit Docking ◽

Induced Fit ◽

Explorative Study ◽

Binding Free Energy Calculation

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Insight to the molecular mechanisms of the osmolyte effects on Mycobacterium tuberculosis pyrazinamidase stability using experimental studies, molecular dynamics simulations, and free energy calculation

International Journal of Mycobacteriology ◽

10.4103/ijmy.ijmy_64_18 ◽

2018 ◽

Vol 7 (3) ◽

pp. 268 ◽

Cited By ~ 4

Author(s):

Faramarz Mehrnejad ◽

Farahnoosh Doustdar ◽

Mohadese Khajehzadeh ◽

Saeedeh Khaleghnejad ◽

Mohammad Pazhang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Mycobacterium Tuberculosis ◽

Molecular Dynamics Simulations ◽

Molecular Mechanisms ◽

Experimental Studies ◽

Free Energy Calculation ◽

Energy Calculation ◽

Dynamics Simulations

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Free energy calculation from steered molecular dynamics simulations using Jarzynski’s equality

The Journal of Chemical Physics ◽

10.1063/1.1590311 ◽

2003 ◽

Vol 119 (6) ◽

pp. 3559-3566 ◽

Cited By ~ 501

Author(s):

Sanghyun Park ◽

Fatemeh Khalili-Araghi ◽

Emad Tajkhorshid ◽

Klaus Schulten

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Steered Molecular Dynamics ◽

Free Energy Calculation ◽

Energy Calculation ◽

Dynamics Simulations ◽

Jarzynski’S Equality

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Parallel cascade selection molecular dynamics for efficient conformational sampling and free energy calculation of proteins

10.1063/1.4968639 ◽

2016 ◽

Cited By ~ 8

Author(s):

Akio Kitao ◽

Ryuhei Harada ◽

Yasutaka Nishihara ◽

Duy Phuoc Tran

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Free Energy Calculation ◽

Conformational Sampling ◽

Energy Calculation

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3D-QSAR, docking, molecular dynamics simulation and free energy calculation studies of some pyrimidine derivatives as novel JAK3 inhibitors

Arabian Journal of Chemistry ◽

10.1016/j.arabjc.2017.09.009 ◽

2020 ◽

Vol 13 (1) ◽

pp. 1052-1078 ◽

Cited By ~ 9

Author(s):

Anand Balupuri ◽

Pavithra K. Balasubramanian ◽

Seung Joo Cho

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

3D Qsar ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Pyrimidine Derivatives

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Extra precision glide docking, free energy calculation and molecular dynamics studies of 1,2-diarylethane derivatives as potent urease inhibitors

Journal of Molecular Modeling ◽

10.1007/s00894-018-3787-4 ◽

2018 ◽

Vol 24 (9) ◽

Cited By ~ 2

Author(s):

Sheetal Gupta ◽

A. V. Bajaj

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Free Energy Calculation ◽

Energy Calculation ◽

Urease Inhibitors ◽

Glide Docking

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Efficient Free-Energy Calculation of Proton Transfer by Constrained Density Functional Theory and Geometrically Restrained Molecular Dynamics Simulation

Chemistry Letters ◽

10.1246/cl.210132 ◽

2021 ◽

Author(s):

Tatsuya Joutsuka ◽

Koji Ando

Keyword(s):

Molecular Dynamics ◽

Density Functional Theory ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Proton Transfer ◽

Density Functional ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Functional Theory

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Molecular Basis of the Interaction for an Essential Subunit PA−PB1 in Influenza Virus RNA Polymerase: Insights from Molecular Dynamics Simulation and Free Energy Calculation

Molecular Pharmaceutics ◽

10.1021/mp900131p ◽

2009 ◽

Vol 7 (1) ◽

pp. 75-85 ◽

Cited By ~ 57

Author(s):

Huanxiang Liu ◽

Xiaojun Yao

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Influenza Virus ◽

Molecular Dynamics Simulation ◽

Molecular Basis ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Virus Rna ◽

Essential Subunit

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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

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A relative free energy calculation method with ion screening effect using molecular dynamics simulation

Journal of Molecular Graphics ◽

10.1016/0263-7855(94)80025-1 ◽

1994 ◽

Vol 12 (1) ◽

pp. 56-57

Author(s):

K. Tazaki ◽

J. Doi

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Calculation Method ◽

Dynamics Simulation ◽

Free Energy Calculation ◽

Energy Calculation ◽

Screening Effect ◽

Relative Free Energy

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