Homology modeling and molecular dynamics simulations of MUC1-9/H-2Kb complex suggest novel binding interactions

Athanassios Stavrakoudis; Ioannis G. Tsoulos; Katalin Uray; Ferenc Hudecz; Vasso Apostolopoulos

doi:10.1007/s00894-010-0884-4

Homology modeling and molecular dynamics simulations of MUC1-9/H-2Kb complex suggest novel binding interactions

Journal of Molecular Modeling ◽

10.1007/s00894-010-0884-4 ◽

2010 ◽

Vol 17 (7) ◽

pp. 1817-1829 ◽

Cited By ~ 3

Author(s):

Athanassios Stavrakoudis ◽

Ioannis G. Tsoulos ◽

Katalin Uray ◽

Ferenc Hudecz ◽

Vasso Apostolopoulos

Keyword(s):

Molecular Dynamics ◽

Homology Modeling ◽

Molecular Dynamics Simulations ◽

Binding Interactions ◽

Dynamics Simulations

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Toward Selective Histone Deacetylase Inhibitor Design: Homology Modeling, Docking Studies, and Molecular Dynamics Simulations of Human Class I Histone Deacetylases

Journal of Medicinal Chemistry ◽

10.1021/jm0505011 ◽

2005 ◽

Vol 48 (22) ◽

pp. 6936-6947 ◽

Cited By ~ 146

Author(s):

Di-Fei Wang ◽

Paul Helquist ◽

Norbert L. Wiech ◽

Olaf Wiest

Keyword(s):

Molecular Dynamics ◽

Homology Modeling ◽

Molecular Dynamics Simulations ◽

Histone Deacetylase ◽

Histone Deacetylase Inhibitor ◽

Histone Deacetylases ◽

Docking Studies ◽

Human Class ◽

Deacetylase Inhibitor ◽

Dynamics Simulations

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Insight into the interaction mechanism of human SGLT2 with its inhibitors: 3D-QSAR studies, homology modeling, and molecular docking and molecular dynamics simulations

Journal of Molecular Modeling ◽

10.1007/s00894-018-3582-2 ◽

2018 ◽

Vol 24 (4) ◽

Cited By ~ 2

Author(s):

Lili Dong ◽

Ruirui Feng ◽

Jiawei Bi ◽

Shengqiang Shen ◽

Huizhe Lu ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Docking ◽

Homology Modeling ◽

Molecular Dynamics Simulations ◽

Interaction Mechanism ◽

3D Qsar ◽

Qsar Studies ◽

Dynamics Simulations ◽

Insight Into

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Computational design of novel fullerene analogues as potential HIV-1 PR inhibitors: Analysis of the binding interactions between fullerene inhibitors and HIV-1 PR residues using 3D QSAR, molecular docking and molecular dynamics simulations

Bioorganic & Medicinal Chemistry ◽

10.1016/j.bmc.2008.10.039 ◽

2008 ◽

Vol 16 (23) ◽

pp. 9957-9974 ◽

Cited By ~ 64

Author(s):

Serdar Durdagi ◽

Thomas Mavromoustakos ◽

Nikos Chronakis ◽

Manthos G. Papadopoulos

Keyword(s):

Molecular Dynamics ◽

Molecular Docking ◽

Molecular Dynamics Simulations ◽

Computational Design ◽

3D Qsar ◽

Binding Interactions ◽

Dynamics Simulations ◽

Hiv 1

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Homology modeling and molecular dynamics simulations of the α1 glycine receptor reveals different states of the channel

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.21435 ◽

2007 ◽

Vol 68 (2) ◽

pp. 581-593 ◽

Cited By ~ 28

Author(s):

Mary Hongying Cheng ◽

Michael Cascio ◽

Rob D. Coalson

Keyword(s):

Molecular Dynamics ◽

Homology Modeling ◽

Molecular Dynamics Simulations ◽

Glycine Receptor ◽

Dynamics Simulations

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Homology Modeling and Molecular Dynamics Simulations of the Mu Opioid Receptor in a Membrane-Aqueous System

ChemBioChem ◽

10.1002/cbic.200400207 ◽

2005 ◽

Vol 6 (5) ◽

pp. 853-859 ◽

Cited By ~ 32

Author(s):

Yan Zhang ◽

Yuk Y. Sham ◽

Ramkumar Rajamani ◽

Jiali Gao ◽

Philip S. Portoghese

Keyword(s):

Molecular Dynamics ◽

Homology Modeling ◽

Molecular Dynamics Simulations ◽

Opioid Receptor ◽

Mu Opioid Receptor ◽

Aqueous System ◽

Mu Opioid ◽

Dynamics Simulations

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Homology modeling of the human 5-HT1A, 5-HT2A, D1, and D2 receptors: model refinement with molecular dynamics simulations and docking evaluation

Journal of Molecular Modeling ◽

10.1007/s00894-012-1368-5 ◽

2012 ◽

Vol 18 (8) ◽

pp. 3639-3655 ◽

Cited By ~ 18

Author(s):

Beow Keat Yap ◽

Michael J. C. Buckle ◽

Stephen W. Doughty

Keyword(s):

Molecular Dynamics ◽

Homology Modeling ◽

Molecular Dynamics Simulations ◽

D2 Receptors ◽

Model Refinement ◽

D1 And D2 Receptors ◽

Dynamics Simulations

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Binding mechanism between Hsp90 and Sgt1 explored by homology modeling and molecular dynamics simulations in rice

Journal of Molecular Modeling ◽

10.1007/s00894-012-1464-6 ◽

2012 ◽

Vol 18 (10) ◽

pp. 4665-4673 ◽

Cited By ~ 9

Author(s):

Jun-jie Yan ◽

Yu-bo Zhang ◽

Yi Ding

Keyword(s):

Molecular Dynamics ◽

Homology Modeling ◽

Molecular Dynamics Simulations ◽

Binding Mechanism ◽

Dynamics Simulations

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Homology modeling and molecular dynamics simulations of the N-terminal domain of wheat high molecular weight glutenin subunit 10

Protein Science ◽

10.1110/ps.0229803 ◽

2003 ◽

Vol 12 (1) ◽

pp. 34-43 ◽

Cited By ~ 10

Author(s):

R. Cazalis

Keyword(s):

Molecular Dynamics ◽

Molecular Weight ◽

Homology Modeling ◽

Molecular Dynamics Simulations ◽

High Molecular Weight ◽

Glutenin Subunit ◽

Terminal Domain ◽

Dynamics Simulations

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Homology modeling and molecular dynamics simulations of lymphotactin

Protein Science ◽

10.1110/ps.9.11.2192 ◽

2000 ◽

Vol 9 (11) ◽

pp. 2192-2199 ◽

Cited By ~ 2

Author(s):

Buyong Ma ◽

Junjie Xiong ◽

Jacek Lubkowski ◽

Ruth Nussinov

Keyword(s):

Molecular Dynamics ◽

Homology Modeling ◽

Molecular Dynamics Simulations ◽

Dynamics Simulations

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Foundations of Biomolecular Simulations: A Critical Introduction to Homology Modeling, Molecular Dynamics Simulations, and Free Energy Calculations of Membrane Proteins

Membrane Proteins Production for Structural Analysis ◽

10.1007/978-1-4939-0662-8_13 ◽

2014 ◽

pp. 347-392

Author(s):

Jérôme Hénin ◽

Marc Baaden ◽

Antoine Taly

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Membrane Proteins ◽

Homology Modeling ◽

Molecular Dynamics Simulations ◽

Free Energy Calculations ◽

Energy Calculations ◽

Biomolecular Simulations ◽

Dynamics Simulations

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