Faculty Opinions recommendation of Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: the role of intermolecular hydrodynamic interactions in barnase-barstar association.

Coarse Grained ◽

Association Rate ◽

Protein Association ◽

Dynamics Simulations ◽

Brownian Dynamics Simulations ◽

Faculty Opinions recommendation of Absolute protein-protein association rate constants from flexible, coarse-grained Brownian dynamics simulations: the role of intermolecular hydrodynamic interactions in barnase-barstar association.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.6916959.7106057 ◽

2010 ◽

Author(s):

Chandra Verma ◽

Gloria Fuentes

Keyword(s):

Rate Constants ◽

Brownian Dynamics ◽

Coarse Grained ◽

Association Rate ◽

Protein Association ◽

Dynamics Simulations ◽

Brownian Dynamics Simulations ◽

Absolute Protein-Protein Association Rate Constants from Flexible, Coarse-Grained Brownian Dynamics Simulations: The Role of Intermolecular Hydrodynamic Interactions in Barnase-Barstar Association

Biophysical Journal ◽

10.1016/j.bpj.2010.09.006 ◽

2010 ◽

Vol 99 (9) ◽

pp. L75-L77 ◽

Cited By ~ 66

Author(s):

Tamara Frembgen-Kesner ◽

Adrian H. Elcock

Keyword(s):

Rate Constants ◽

Brownian Dynamics ◽

Coarse Grained ◽

Association Rate ◽

Protein Association ◽

Dynamics Simulations ◽

Brownian Dynamics Simulations ◽

Computing Protein-Ligand Binding Association Rate Constants by Combining Brownian Dynamics and Molecular Dynamics Simulations

Biophysical Journal ◽

10.1016/j.bpj.2017.11.357 ◽

2018 ◽

Vol 114 (3) ◽

pp. 56a

Author(s):

S. Kashif Sadiq ◽

Rebecca C. Wade

Keyword(s):

Molecular Dynamics ◽

Ligand Binding ◽

Molecular Dynamics Simulations ◽

Rate Constants ◽

Brownian Dynamics ◽

Association Rate ◽

Dynamics Simulations ◽

Molecule-Centered Method for Accelerating the Calculation of Hydrodynamic Interactions in Brownian Dynamics Simulations Containing Many Flexible Biomolecules

Journal of Chemical Theory and Computation ◽

10.1021/ct400240w ◽

2013 ◽

Vol 9 (7) ◽

pp. 3224-3239 ◽

Cited By ~ 8

Author(s):

Adrian H. Elcock

Keyword(s):

Brownian Dynamics ◽

Dynamics Simulations ◽

An iterative method for hydrodynamic interactions in Brownian dynamics simulations of polymer dynamics

The Journal of Chemical Physics ◽

10.1063/1.4993218 ◽

2017 ◽

Vol 147 (2) ◽

pp. 024904 ◽

Cited By ~ 9

Author(s):

Linling Miao ◽

Charles D. Young ◽

Charles E. Sing

Keyword(s):

Iterative Method ◽

Brownian Dynamics ◽

Polymer Dynamics ◽

Dynamics Simulations ◽

Coarse-Grained Brownian Dynamics Simulations of the 10-23 DNAzyme

Biophysical Journal ◽

10.1016/j.bpj.2009.09.003 ◽

2009 ◽

Vol 97 (10) ◽

pp. 2785-2793 ◽

Cited By ~ 14

Author(s):

Martin Kenward ◽

Kevin D. Dorfman

Keyword(s):

Brownian Dynamics ◽

Coarse Grained ◽

Dynamics Simulations ◽

BDflex: A method for efficient treatment of molecular flexibility in calculating protein-ligand binding rate constants from Brownian dynamics simulations

The Journal of Chemical Physics ◽

10.1063/1.4756913 ◽

2012 ◽

Vol 137 (13) ◽

pp. 135105 ◽

Cited By ~ 13

Author(s):

Nicholas Greives ◽

Huan-Xiang Zhou

Keyword(s):

Ligand Binding ◽

Rate Constants ◽

Brownian Dynamics ◽

Molecular Flexibility ◽

Efficient Treatment ◽

Binding Rate ◽

Dynamics Simulations ◽

Brownian Dynamics Simulations of Dendrimers under Elongational Flow: Bead−Rod Model with Hydrodynamic Interactions

Macromolecules ◽

10.1021/ma030088b ◽

2003 ◽

Vol 36 (18) ◽

pp. 6914-6924 ◽

Cited By ~ 23

Author(s):

Igor M. Neelov ◽

David B. Adolf

Keyword(s):

Brownian Dynamics ◽

Elongational Flow ◽

Rod Model ◽

Dynamics Simulations ◽

Coarse-Grained Brownian Dynamics Simulations of Electrophoresis of DNA Molecules from Generalized Reptation Models

Macromolecules ◽

10.1021/ma061912+ ◽

2007 ◽

Vol 40 (2) ◽

pp. 366-378 ◽

Cited By ~ 4

Author(s):

Richard S. Graham ◽

Ronald G. Larson

Keyword(s):

Brownian Dynamics ◽

Coarse Grained ◽

Dna Molecules ◽

Dynamics Simulations ◽

Brownian dynamics simulations of the effects of hydrodynamic interactions on the polymer viscoelastic behavior

Polymer ◽

10.1016/s0032-3861(03)00152-6 ◽

2003 ◽

Vol 44 (9) ◽

pp. 2807-2815 ◽

Cited By ~ 3

Author(s):

D.-J. Yang ◽

Y.-H. Lin

Keyword(s):

Brownian Dynamics ◽

Viscoelastic Behavior ◽

Dynamics Simulations ◽