Binding selectivity studies of PKBα using molecular dynamics simulation and free energy calculations

Journal of Molecular Modeling ◽

10.1007/s00894-013-1997-3 ◽

2013 ◽

Vol 19 (11) ◽

pp. 5097-5112 ◽

Author(s):

Shi-Feng Chen ◽

Yang Cao ◽

Jiong-Jiong Chen ◽

Jian-Zhong Chen

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Free Energy Calculations ◽

Dynamics Simulation ◽

Binding Selectivity ◽

Energy Calculations ◽

Selectivity Studies

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Refinement of X-ray data on dual cosubstrate specificity of CK2 kinase by free energy calculations based on molecular dynamics simulation

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20350 ◽

2004 ◽

Vol 58 (3) ◽

pp. 511-517 ◽

Author(s):

Piotr Setny ◽

Maciej Geller

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Free Energy Calculations ◽

Dynamics Simulation ◽

Energy Calculations ◽

X Ray ◽

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The molecular mechanism studies of chirality effect of PHA-739358 on Aurora kinase A by molecular dynamics simulation and free energy calculations

Journal of Computer-Aided Molecular Design ◽

10.1007/s10822-010-9408-7 ◽

2011 ◽

Vol 25 (2) ◽

pp. 171-180 ◽

Author(s):

Yuanhua Cheng ◽

Wei Cui ◽

Quan Chen ◽

Chen-Ho Tung ◽

Mingjuan Ji ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Molecular Mechanism ◽

Aurora Kinase ◽

Free Energy Calculations ◽

Dynamics Simulation ◽

Aurora Kinase A ◽

Energy Calculations ◽

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Molecular dynamics simulation and free energy calculations of symmetric fluoro-substituted diol-based HIV-1 protease inhibitors

Journal of Molecular Structure THEOCHEM ◽

10.1016/j.theochem.2008.11.029 ◽

2009 ◽

Vol 899 (1-3) ◽

pp. 1-8 ◽

Author(s):

Jian-Zhong Chen ◽

Mao-You Yang ◽

Chang-Hong Yi ◽

Shu-Hua Shi ◽

Qing-Gang Zhang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Protease Inhibitors ◽

Free Energy Calculations ◽

Dynamics Simulation ◽

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 ◽

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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Some practical aspects of free energy calculations from molecular dynamics simulation

Journal of Computational Chemistry ◽

10.1002/(sici)1096-987x(199906)20:8<877::aid-jcc12>3.0.co;2-o ◽

1999 ◽

Vol 20 (8) ◽

pp. 877-885 ◽

Author(s):

Srikanta Sen ◽

Lennart Nilsson

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Free Energy Calculations ◽

Dynamics Simulation ◽

Energy Calculations

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Probing the interaction mechanism of small molecule inhibitors with matriptase based on molecular dynamics simulation and free energy calculations

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2016.1160259 ◽

2016 ◽

Vol 35 (4) ◽

pp. 755-764 ◽

Author(s):

Dong-Ru Sun ◽

Qing-Chuan Zheng ◽

Hong-Xing Zhang

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Small Molecule ◽

Small Molecule Inhibitors ◽

Interaction Mechanism ◽

Free Energy Calculations ◽

Dynamics Simulation ◽

Energy Calculations

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Free energy calculations for Lennard-Jones systems and water using the expanded ensemble method A Monte Carlo and molecular dynamics simulation study

Molecular Physics ◽

10.1080/00268979400100344 ◽

1994 ◽

Vol 82 (3) ◽

pp. 455-471 ◽

Author(s):

Alexander P. Lyubartsev ◽

Aatto Laaksonen ◽

Pavel N. Vorontsov-Velyaminov

Keyword(s):

Molecular Dynamics ◽

Monte Carlo ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Simulation Study ◽

Free Energy Calculations ◽

Dynamics Simulation ◽

Energy Calculations ◽

Lennard Jones ◽

Expanded Ensemble

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Receptor-guided 3D-QSAR studies, molecular dynamics simulation and free energy calculations of Btk kinase inhibitors

BMC Systems Biology ◽

10.1186/s12918-017-0385-5 ◽

2017 ◽

Vol 11 (S2) ◽

Author(s):

Pavithra K. Balasubramanian ◽

Anand Balupuri ◽

Hee-Young Kang ◽

Seung Joo Cho

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Kinase Inhibitors ◽

3D Qsar ◽

Free Energy Calculations ◽

Dynamics Simulation ◽

Energy Calculations ◽

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Computational simulation studies on the binding selectivity of Wee1 and Checkpoint kinase 1 by molecular dynamics simulation combined with free energy calculations

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2020.1823882 ◽

2020 ◽

pp. 1-10

Author(s):

Yaping Li ◽

Xingyong Liu ◽

Shuqun Zhang ◽

Liangliang Wang ◽

Li Zhang ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Computational Simulation ◽

Free Energy Calculations ◽

Dynamics Simulation ◽

Simulation Studies ◽

Checkpoint Kinase ◽

Energy Calculations ◽

Checkpoint Kinase 1

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Molecular Dynamics Simulation Study on CO2 Physical Absorption Mechanisms for Ethylene-Glycol-Based Solvents Using Free Energy Calculations

Industrial & Engineering Chemistry Research ◽

10.1021/acs.iecr.6b01074 ◽

2016 ◽

Vol 55 (29) ◽

pp. 8200-8206 ◽

Author(s):

Ryo Nagumo ◽

Yukihiro Muraki ◽

Shuichi Iwata ◽

Hideki Mori ◽

Hiromitsu Takaba ◽

...

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulation ◽

Ethylene Glycol ◽

Simulation Study ◽

Free Energy Calculations ◽

Dynamics Simulation ◽

Energy Calculations ◽

Physical Absorption

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