Fully Flexible Docking via Reaction-Coordinate-Independent Molecular Dynamics Simulations

Martina Bertazzo; Mattia Bernetti; Maurizio Recanatini; Matteo Masetti; Andrea Cavalli

doi:10.1021/acs.jcim.7b00674

Fully Flexible Docking via Reaction-Coordinate-Independent Molecular Dynamics Simulations

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.7b00674 ◽

2018 ◽

Vol 58 (2) ◽

pp. 490-500 ◽

Cited By ~ 8

Author(s):

Martina Bertazzo ◽

Mattia Bernetti ◽

Maurizio Recanatini ◽

Matteo Masetti ◽

Andrea Cavalli

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Reaction Coordinate ◽

Flexible Docking ◽

Dynamics Simulations

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Sampling the Proton Transfer Reaction Coordinate in Mixed Quantum-Classical Molecular Dynamics Simulations

The Journal of Physical Chemistry A ◽

10.1021/jp206772e ◽

2012 ◽

Vol 116 (2) ◽

pp. 832-838 ◽

Cited By ~ 3

Author(s):

Being J. Ka ◽

Ward H. Thompson

Keyword(s):

Molecular Dynamics ◽

Proton Transfer ◽

Molecular Dynamics Simulations ◽

Transfer Reaction ◽

Proton Transfer Reaction ◽

Reaction Coordinate ◽

Classical Molecular Dynamics ◽

Dynamics Simulations

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Investigation of the complex reaction coordinate of acid catalyzed amide hydrolysis from molecular dynamics simulations

Chemical Physics ◽

10.1016/j.chemphys.2004.01.016 ◽

2004 ◽

Vol 300 (1-3) ◽

pp. 79-83 ◽

Cited By ~ 13

Author(s):

Dirk Zahn

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Reaction Coordinate ◽

Complex Reaction ◽

Amide Hydrolysis ◽

Acid Catalyzed ◽

Dynamics Simulations

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1P048 Flexible docking multicanonical molecular dynamics simulations between factor Xa and its inhibitors(1. Protein structure and dynamics (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Seibutsu Butsuri ◽

10.2142/biophys.46.s158_4 ◽

2006 ◽

Vol 46 (supplement2) ◽

pp. S158

Author(s):

Narutoshi Kamiya ◽

Yasushige Yonezawa ◽

Haruki Nakamura

Keyword(s):

Molecular Dynamics ◽

Protein Structure ◽

Molecular Dynamics Simulations ◽

Poster Session ◽

Factor Xa ◽

Flexible Docking ◽

Structure And Dynamics ◽

Meeting Program ◽

Dynamics Simulations ◽

Protein Structure And Dynamics

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Enantiomeric Transitions in the Chiral Cluster Au15 Studied by a Reaction Coordinate Deduced from Molecular Dynamics Simulations

The Journal of Physical Chemistry A ◽

10.1021/acs.jpca.0c05099 ◽

2020 ◽

Vol 124 (42) ◽

pp. 8679-8691 ◽

Cited By ~ 1

Author(s):

Chong Chiat Lim ◽

San Kiong Lai

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Reaction Coordinate ◽

Dynamics Simulations

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Combining Pharmacophore Search, Automated Docking, and Molecular Dynamics Simulations as a Novel Strategy for Flexible Docking. Proof of Concept: Docking of Arginine−Glycine−Aspartic Acid-like Compounds into the αvβ3Binding Site

Journal of Medicinal Chemistry ◽

10.1021/jm0311386 ◽

2004 ◽

Vol 47 (17) ◽

pp. 4178-4187 ◽

Cited By ~ 44

Author(s):

Nicolas Moitessier ◽

Christophe Henry ◽

Bernard Maigret ◽

Yves Chapleur

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Aspartic Acid ◽

Proof Of Concept ◽

Flexible Docking ◽

Automated Docking ◽

Arginine Glycine Aspartic Acid ◽

Novel Strategy ◽

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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Nonequilibrium Molecular Dynamics Simulations of 3-Methylhexane: The Effect of Inter- and Intramolecular Potential Models on Simulated Viscosity

The Journal of Physical Chemistry A ◽

10.1021/jp971476g ◽

1997 ◽

Vol 101 (27) ◽

pp. 5026-5026

Author(s):

Maija Lahtela ◽

Tapani A. Pakkanen ◽

Richard L. Rowley

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Nonequilibrium Molecular Dynamics ◽

Potential Models ◽

Dynamics Simulations

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Assessment of all-atom potentials for modeling membranes: molecular dynamics simulations of solid and liquid alkanes and crystals of phospholipid fragments

Journal de Chimie Physique ◽

10.1051/jcp/1997941482 ◽

1997 ◽

Vol 94 ◽

pp. 1482-1502 ◽

Cited By ~ 27

Author(s):

DJ Tobias ◽

K Tu ◽

ML Klein

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Dynamics Simulations ◽

Liquid Alkanes

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