Explaining the inhibition of cyclin-dependent kinase 5 by peptides derived from p25 with molecular dynamics simulations and MM-PBSA

Vincent B. C. Tan; Bing Zhang; Kian Meng Lim; Tong Earn Tay

doi:10.1007/s00894-009-0514-1

Explaining the inhibition of cyclin-dependent kinase 5 by peptides derived from p25 with molecular dynamics simulations and MM-PBSA

Journal of Molecular Modeling ◽

10.1007/s00894-009-0514-1 ◽

2009 ◽

Vol 16 (1) ◽

pp. 1-8 ◽

Cited By ~ 9

Author(s):

Vincent B. C. Tan ◽

Bing Zhang ◽

Kian Meng Lim ◽

Tong Earn Tay

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Cyclin Dependent Kinase ◽

Dynamics Simulations ◽

Cyclin Dependent Kinase 5

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Steered Molecular Dynamics Simulations for Studying Protein–Ligand Interaction in Cyclin-Dependent Kinase 5

Journal of Chemical Information and Modeling ◽

10.1021/ci4003574 ◽

2014 ◽

Vol 54 (2) ◽

pp. 470-480 ◽

Cited By ~ 89

Author(s):

Jagdish Suresh Patel ◽

Anna Berteotti ◽

Simone Ronsisvalle ◽

Walter Rocchia ◽

Andrea Cavalli

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Steered Molecular Dynamics ◽

Cyclin Dependent Kinase ◽

Ligand Interaction ◽

Protein Ligand Interaction ◽

Dynamics Simulations ◽

Cyclin Dependent Kinase 5

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Studying the mechanism that enables paullones to selectively inhibit glycogen synthase kinase 3 rather than cyclin-dependent kinase 5 by molecular dynamics simulations and free-energy calculations

Journal of Molecular Modeling ◽

10.1007/s00894-010-0762-0 ◽

2010 ◽

Vol 17 (4) ◽

pp. 795-803 ◽

Cited By ~ 11

Author(s):

Quan Chen ◽

Wei Cui ◽

Yuanhua Cheng ◽

Fushi Zhang ◽

Mingjuan Ji

Keyword(s):

Molecular Dynamics ◽

Free Energy ◽

Molecular Dynamics Simulations ◽

Glycogen Synthase ◽

Free Energy Calculations ◽

Glycogen Synthase Kinase 3 ◽

Cyclin Dependent Kinase ◽

Energy Calculations ◽

Dynamics Simulations ◽

Cyclin Dependent Kinase 5

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Investigation of the newly characterized baimantuoluoamide a and baimantuoluoamide b alkaloids as potential cyclin-dependent kinase 4 (CDK4) inhibitors using molecular docking and molecular dynamics simulations

Journal of Molecular Structure ◽

10.1016/j.molstruc.2021.129925 ◽

2021 ◽

Vol 1230 ◽

pp. 129925

Author(s):

K. Gurushankar ◽

Hrvoje Rimac ◽

V. Potemkin ◽

M. Grishina

Keyword(s):

Molecular Dynamics ◽

Molecular Docking ◽

Molecular Dynamics Simulations ◽

Cyclin Dependent Kinase ◽

Dynamics Simulations

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Regulatory phosphorylation of cyclin-dependent kinase 2: insights from molecular dynamics simulations

Journal of Molecular Modeling ◽

10.1007/s00894-008-0312-1 ◽

2008 ◽

Vol 14 (8) ◽

pp. 761-768 ◽

Cited By ~ 10

Author(s):

Iveta Bártová ◽

Jaroslav Koča ◽

Michal Otyepka

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Cyclin Dependent Kinase ◽

Regulatory Phosphorylation ◽

Dynamics Simulations

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New Scoring Functions for Virtual Screening from Molecular Dynamics Simulations with a Quantum-Refined Force-Field (QRFF-MD). Application to Cyclin-Dependent Kinase 2

Journal of Chemical Information and Modeling ◽

10.1021/ci050289+ ◽

2006 ◽

Vol 46 (1) ◽

pp. 254-263 ◽

Cited By ~ 19

Author(s):

Ph. Ferrara ◽

A. Curioni ◽

E. Vangrevelinghe ◽

T. Meyer ◽

T. Mordasini ◽

...

Keyword(s):

Molecular Dynamics ◽

Virtual Screening ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Scoring Functions ◽

Cyclin Dependent Kinase ◽

Dynamics Simulations ◽

New Scoring

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New Scoring Functions for Virtual Screening from Molecular Dynamics Simulations with a Quantum-Refined Force-Field (QRFF-MD). Application to Cyclin-Dependent Kinase 2.

ChemInform ◽

10.1002/chin.200617221 ◽

2006 ◽

Vol 37 (17) ◽

Author(s):

Ph. Ferrara ◽

A. Curioni ◽

E. Vangrevelinghe ◽

T. Meyer ◽

T. Mordasini ◽

...

Keyword(s):

Molecular Dynamics ◽

Virtual Screening ◽

Force Field ◽

Molecular Dynamics Simulations ◽

Scoring Functions ◽

Cyclin Dependent Kinase ◽

Dynamics Simulations ◽

New Scoring

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Molecular dynamics simulations reveal the determinants of cyclin-dependent kinase 2 inhibition by 5-nitrosopyrimidine derivatives

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2019.1666032 ◽

2019 ◽

Vol 38 (13) ◽

pp. 4016-4024

Author(s):

Stefano Guglielmo ◽

Daniela Cortese ◽

Celine Cano ◽

Roberta Fruttero

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Cyclin Dependent Kinase ◽

Dynamics Simulations

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Structure of phosphorus-selenium glasses: results from ab initio molecular dynamics simulations

Molecular Physics ◽

10.1080/002689700162045 ◽

2000 ◽

Vol 98 (11) ◽

pp. 701-707

Author(s):

Alessandro Sergi, Mauro Ferrario, Francesco Bu

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Molecular Dynamics Simulations ◽

Ab Initio Molecular Dynamics ◽

Dynamics Simulations

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Tracer diffusion in perfectly aligned liquid crystalline phases Kinetic theory and molecular dynamics simulations

Molecular Physics ◽

10.1080/00268979709482789 ◽

1997 ◽

Vol 91 (6) ◽

pp. 993-1003 ◽

Cited By ~ 1

Author(s):

ANJALI KHARE ◽

DAVID KOFKE ◽

GLENN EVANS

Keyword(s):

Molecular Dynamics ◽

Kinetic Theory ◽

Molecular Dynamics Simulations ◽

Liquid Crystalline ◽

Tracer Diffusion ◽

Crystalline Phases ◽

Liquid Crystalline Phases ◽

Dynamics Simulations

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ERRATUM Molecular dynamics simulations of liquid crystal phases using atomistic potentials

Molecular Physics ◽

10.1080/002689798167430 ◽

1998 ◽

Vol 95 (1) ◽

pp. 121-121

Author(s):

CARL MCBRIDE MARK R. WILSON JUDITH A. K.

Keyword(s):

Molecular Dynamics ◽

Liquid Crystal ◽

Molecular Dynamics Simulations ◽

Crystal Phases ◽

Dynamics Simulations ◽

Liquid Crystal Phases

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