Calculation of ligand-nucleic acid binding free energies with the generalized-born model in DOCK

Biopolymers ◽

10.1002/bip.10541 ◽

2004 ◽

Vol 73 (2) ◽

pp. 192-204 ◽

Author(s):

Xinshan Kang ◽

Richard H. Shafer ◽

Irwin D. Kuntz

Keyword(s):

Nucleic Acid ◽

Nucleic Acid Binding ◽

Free Energies ◽

Generalized Born ◽

Generalized Born Model ◽

Binding Free Energies

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Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.7b00192 ◽

2017 ◽

Vol 57 (10) ◽

pp. 2505-2513 ◽

Author(s):

Negin Forouzesh ◽

Saeed Izadi ◽

Alexey V. Onufriev

Keyword(s):

Free Energies ◽

Generalized Born ◽

Electrostatic Binding ◽

Generalized Born Model ◽

Binding Free Energies

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A Stochastic Technique that Computes Electrostatic Solvation and Binding Free Energies in the Generalized Born Model with Exact Born Radii

Biophysical Journal ◽

10.1016/j.bpj.2011.11.916 ◽

2012 ◽

Vol 102 (3) ◽

pp. 168a-169a

Author(s):

Robert C. Harris ◽

Marcia O. Fenley

Keyword(s):

Free Energies ◽

Generalized Born ◽

Generalized Born Model ◽

Binding Free Energies

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Free Energies of Hydration from a Generalized Born Model and an All-Atom Force Field

The Journal of Physical Chemistry B ◽

10.1021/jp0484579 ◽

2004 ◽

Vol 108 (41) ◽

pp. 16264-16270 ◽

Author(s):

William L. Jorgensen ◽

Jakob P. Ulmschneider ◽

Julian Tirado-Rives

Keyword(s):

Force Field ◽

Free Energies ◽

Generalized Born ◽

Generalized Born Model

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Accuracy assessment of the linear Poisson-Boltzmann equation and reparametrization of the OBC generalized Born model for nucleic acids and nucleic acid-protein complexes

Journal of Computational Chemistry ◽

10.1002/jcc.23832 ◽

2015 ◽

Vol 36 (9) ◽

pp. 585-596 ◽

Author(s):

Federico Fogolari ◽

Alessandra Corazza ◽

Gennaro Esposito

Keyword(s):

Boltzmann Equation ◽

Nucleic Acid ◽

Protein Complexes ◽

Accuracy Assessment ◽

Generalized Born ◽

Acid Protein ◽

Generalized Born Model ◽

Poisson Boltzmann ◽

Poisson Boltzmann Equation

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2P129 Critical parameters of the generalized Born model to simulate protein-protein interactions(07. Water & Hydration & Electrolyte,Poster,The 52nd Annual Meeting of the Biophysical Society of Japan(BSJ2014))

Seibutsu Butsuri ◽

10.2142/biophys.54.s216_3 ◽

2014 ◽

Vol 54 (supplement1-2) ◽

pp. S216

Author(s):

Yukinobu Mizuhara ◽

Koji Umezawa ◽

Jun Ohnuki ◽

Dan Parkin ◽

Mitsunori Takano

Keyword(s):

Annual Meeting ◽

Protein Interactions ◽

Critical Parameters ◽

Protein Protein Interactions ◽

Generalized Born ◽

Biophysical Society ◽

Generalized Born Model

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Electrostatics of Ligand Binding: Parametrization of the Generalized Born Model and Comparison with the Poisson−Boltzmann Approach

The Journal of Physical Chemistry B ◽

10.1021/jp060334w ◽

2006 ◽

Vol 110 (18) ◽

pp. 9304-9313 ◽

Author(s):

Hao-Yang Liu ◽

Xiaoqin Zou

Keyword(s):

Ligand Binding ◽

Generalized Born ◽

Generalized Born Model ◽

Poisson Boltzmann

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Improvement of accuracy of free-energy landscapes of peptides calculated with generalized Born model by using numerical solutions of Poisson’s equation

Chemical Physics Letters ◽

10.1016/j.cplett.2004.06.096 ◽

2004 ◽

Vol 393 (4-6) ◽

pp. 546-551 ◽

Author(s):

Takanori Ishizuka ◽

Tohru Terada ◽

Shugo Nakamura ◽

Kentaro Shimizu

Keyword(s):

Free Energy ◽

Numerical Solutions ◽

Poisson’S Equation ◽

Energy Landscapes ◽

Poisson's Equation ◽

Generalized Born ◽

Generalized Born Model ◽

Free Energy Landscapes

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Modification of the Generalized Born Model Suitable for Macromolecules

The Journal of Physical Chemistry B ◽

10.1021/jp994072s ◽

2000 ◽

Vol 104 (15) ◽

pp. 3712-3720 ◽

Author(s):

Alexey Onufriev ◽

Donald Bashford ◽

David A. Case

Keyword(s):

Generalized Born ◽

Generalized Born Model

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The treatment of solvation by a generalized Born model and a self-consistent charge-density functional theory-based tight-binding method

Journal of Computational Chemistry ◽

10.1002/jcc.10164 ◽

2002 ◽

Vol 23 (15) ◽

pp. 1404-1415 ◽

Author(s):

Li Xie ◽

Haiyan Liu

Keyword(s):

Density Functional Theory ◽

Charge Density ◽

Density Functional ◽

Tight Binding ◽

Functional Theory ◽

Generalized Born ◽

Self Consistent ◽

Tight Binding Method ◽

Generalized Born Model

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Reducing the Secondary Structure Bias in the Generalized Born Model via R6 Effective Radii

Journal of Chemical Theory and Computation ◽

10.1021/ct100392h ◽

2010 ◽

Vol 6 (12) ◽

pp. 3613-3630 ◽

Author(s):

Boris Aguilar ◽

Richard Shadrach ◽

Alexey V. Onufriev

Keyword(s):

Secondary Structure ◽

Generalized Born ◽

Generalized Born Model

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