Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein–DNA Binding Free Energy Landscapes

Morteza Khabiri; Peter L. Freddolino

doi:10.1021/acs.jpcb.6b12450

Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein–DNA Binding Free Energy Landscapes

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.6b12450 ◽

2017 ◽

Vol 121 (20) ◽

pp. 5151-5161 ◽

Cited By ~ 11

Author(s):

Morteza Khabiri ◽

Peter L. Freddolino

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Dna Binding ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Energy Landscapes ◽

Simulation Based ◽

Free Energy Landscapes

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Comment on “Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes”

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.8b04187 ◽

2018 ◽

Vol 124 (6) ◽

pp. 1115-1123

Author(s):

Vytautas Gapsys ◽

Morteza Khabiri ◽

Bert L. de Groot ◽

Peter L. Freddolino

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Dna Binding ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Energy Landscapes ◽

Simulation Based ◽

Free Energy Landscapes

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Correction to “Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein–DNA Binding Free Energy Landscapes”

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.0c10359 ◽

2020 ◽

Vol 124 (49) ◽

pp. 11311-11311

Author(s):

Morteza Khabiri ◽

Peter L. Freddolino

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Dna Binding ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Energy Landscapes ◽

Simulation Based ◽

Free Energy Landscapes

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Analysis of the Free Energy Landscapes for the Opening–Closing Dynamics of the Maltose Transporter ATPase MalK2 Using Enhanced-Sampling Molecular Dynamics Simulation

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.5b05432 ◽

2015 ◽

Vol 119 (30) ◽

pp. 9717-9725 ◽

Cited By ~ 8

Author(s):

Wei-Lin Hsu ◽

Tadaomi Furuta ◽

Minoru Sakurai

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Energy Landscapes ◽

Enhanced Sampling ◽

Maltose Transporter ◽

Free Energy Landscapes

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1P587 Folding free-energy landscapes of 10-residue proteins(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Seibutsu Butsuri ◽

10.2142/biophys.46.s293_3 ◽

2006 ◽

Vol 46 (supplement2) ◽

pp. S293

Author(s):

Daisuke Satoh ◽

Kentaro Shimizu ◽

Shugo Nakamura ◽

Tohru Terada

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Poster Session ◽

Dynamics Simulation ◽

Energy Landscapes ◽

Meeting Program ◽

Free Energy Landscapes ◽

Folding Free Energy

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Free energy landscapes of small peptides in an implicit solvent model determined by force-biased multicanonical molecular dynamics simulation

Chemical Physics Letters ◽

10.1016/j.cplett.2004.10.118 ◽

2004 ◽

Vol 400 (1-3) ◽

pp. 258-263 ◽

Cited By ~ 7

Author(s):

Yukihisa S. Watanabe ◽

Jae Gil Kim ◽

Yoshifumi Fukunishi ◽

Haruki Nakamura

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Dynamics Simulation ◽

Implicit Solvent ◽

Energy Landscapes ◽

Small Peptides ◽

Implicit Solvent Model ◽

Solvent Model ◽

Free Energy Landscapes

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Investigation of binding mechanism and downregulation of elacestrant for wild and L536S mutant estrogen receptor‐α through molecular dynamics simulation and binding free energy analysis

Journal of Computational Chemistry ◽

10.1002/jcc.26076 ◽

2019 ◽

Vol 41 (2) ◽

pp. 97-109 ◽

Cited By ~ 1

Author(s):

Kalaiarasi Chinnasamy ◽

Manjula Saravanan ◽

Kumaradhas Poomani

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Estrogen Receptor ◽

Molecular Dynamics Simulation ◽

Energy Analysis ◽

Binding Free Energy ◽

Estrogen Receptor Α ◽

Dynamics Simulation ◽

Binding Mechanism ◽

Free Energy Analysis

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Insights of inhibition mechanism of sifuvirtide and MT-sifuvirtide against wild and mutant HIV-1 envelope glycoprotein41: a molecular dynamics simulation and binding free energy study

Molecular Simulation ◽

10.1080/08927022.2020.1716978 ◽

2020 ◽

Vol 46 (6) ◽

pp. 429-439

Author(s):

Iruthayaraj Ancy ◽

Magudeeswaran Sivanandam ◽

Raju Kalaivani ◽

Poomani Kumaradhas

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Binding Free Energy ◽

Dynamics Simulation ◽

Inhibition Mechanism ◽

Hiv 1

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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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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

Journal of Biomolecular Structure and Dynamics ◽

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 ◽

Free Energy Calculations ◽

Dynamics Simulation ◽

Binding Mechanism ◽

Binding Free Energy Calculations

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Effects of single-walled carbon nanotube on the conformation of human hepcidin: molecular dynamics simulation and binding free energy calculations

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2018.1477624 ◽

2018 ◽

Vol 37 (8) ◽

pp. 2125-2132 ◽

Cited By ~ 3

Author(s):

Reza Rasoolzadeh ◽

Faramarz Mehrnejad ◽

Majid Taghdir ◽

Parichehreh Yaghmaei

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Carbon Nanotube ◽

Molecular Dynamics Simulation ◽

Binding Free Energy ◽

Free Energy Calculations ◽

Dynamics Simulation ◽

Single Walled Carbon Nanotube ◽

Energy Calculations ◽

Binding Free Energy Calculations

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