Influence of Go-Like Interactions on Global Shapes of Energy Landscapes in β-Barrel Forming Model Proteins:  Inherent Structure Analysis and Statistical Temperature Molecular Dynamics Simulation

Jaegil Kim; Thomas Keyes

doi:10.1021/jp072872u

Influence of Go-Like Interactions on Global Shapes of Energy Landscapes in β-Barrel Forming Model Proteins: Inherent Structure Analysis and Statistical Temperature Molecular Dynamics Simulation

The Journal of Physical Chemistry B ◽

10.1021/jp072872u ◽

2008 ◽

Vol 112 (3) ◽

pp. 954-966 ◽

Cited By ~ 12

Author(s):

Jaegil Kim ◽

Thomas Keyes

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Structure Analysis ◽

Dynamics Simulation ◽

Energy Landscapes ◽

Inherent Structure

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Insight into TPMT∗23 mutation mis-folding using molecular dynamics simulation and protein structure analysis

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2012.721495 ◽

2013 ◽

Vol 31 (10) ◽

pp. 1066-1076 ◽

Cited By ~ 1

Author(s):

Sofiene Larif ◽

Chaker Ben Salem ◽

Zohra Soua ◽

Houssem Hmouda ◽

Kamel Bouraoui

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulation ◽

Structure Analysis ◽

Dynamics Simulation ◽

Protein Structure Analysis ◽

Insight Into

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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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Three dimensional structure analysis of alpha-conotoxin EI(nicotinic acetylcholine receptor antagonist)by molecular dynamics simulation

Seibutsu Butsuri ◽

10.2142/biophys.41.s102_2 ◽

2001 ◽

Vol 41 (supplement) ◽

pp. S102

Author(s):

M. Matsuo ◽

H. Gouda ◽

N. Yamaotsu ◽

S. Hirono

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Receptor Antagonist ◽

Acetylcholine Receptor ◽

Nicotinic Acetylcholine Receptor ◽

Structure Analysis ◽

Three Dimensional ◽

Dynamics Simulation ◽

Dimensional Structure ◽

Nicotinic Acetylcholine

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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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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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Molecular dynamics simulation of the local inherent structure of liquid silicon at different temperatures

Physical Review B ◽

10.1103/physrevb.60.3194 ◽

1999 ◽

Vol 60 (5) ◽

pp. 3194-3199 ◽

Cited By ~ 17

Author(s):

C. S. Liu ◽

Z. G. Zhu ◽

Junchao Xia ◽

D. Y. Sun

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Liquid Silicon ◽

Dynamics Simulation ◽

Inherent Structure ◽

Different Temperatures ◽

Structure Of Liquid

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20ns Molecular Dynamics Simulation of the Antennapedia Homeodomain-DNA Complex: Water Interaction and DNA Structure Analysis

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2010.10507329 ◽

2010 ◽

Vol 27 (4) ◽

pp. 443-455 ◽

Cited By ~ 28

Author(s):

Sujata Roy ◽

Ashoke Ranjan Thakur

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Structure Analysis ◽

Dna Structure ◽

Dynamics Simulation ◽

Water Interaction ◽

Dna Complex

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Computational docking, molecular dynamics simulation and subsite structure analysis of a maltogenic amylase from Bacillus lehensis G1 provide insights into substrate and product specificity

Journal of Molecular Graphics and Modelling ◽

10.1016/j.jmgm.2016.04.004 ◽

2016 ◽

Vol 67 ◽

pp. 1-13 ◽

Cited By ~ 7

Author(s):

Nor Hasmaliana Abdul Manas ◽

Farah Diba Abu Bakar ◽

Rosli Md. Illias

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulation ◽

Structure Analysis ◽

Dynamics Simulation ◽

Computational Docking ◽

Product Specificity ◽

Maltogenic Amylase

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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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