Surface Generalized Born Method: A Simple, Fast, and Precise Implicit Solvent Model beyond the Coulomb Approximation

The Journal of Physical Chemistry A ◽

10.1021/jp046721s ◽

2004 ◽

Vol 108 (43) ◽

pp. 9323-9327 ◽

Author(s):

Alexey N. Romanov ◽

Sergey N. Jabin ◽

Yaroslav B. Martynov ◽

Alexey V. Sulimov ◽

Fedor V. Grigoriev ◽

...

Keyword(s):

Implicit Solvent ◽

Generalized Born ◽

Implicit Solvent Model ◽

Solvent Model ◽

Coulomb Approximation

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Rapid Alchemical Free Energy Calculation Employing a Generalized Born Implicit Solvent Model

The Journal of Physical Chemistry B ◽

10.1021/jp506367y ◽

2014 ◽

Vol 119 (3) ◽

pp. 968-975 ◽

Author(s):

Katja Ostermeir ◽

Martin Zacharias

Keyword(s):

Free Energy ◽

Free Energy Calculation ◽

Implicit Solvent ◽

Energy Calculation ◽

Generalized Born ◽

Implicit Solvent Model ◽

Solvent Model ◽

Alchemical Free Energy

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Molecular dynamics simulations of ionic and nonionic surfactant micelles with a generalized born implicit-solvent model

Journal of Computational Chemistry ◽

10.1002/jcc.21813 ◽

2011 ◽

Vol 32 (11) ◽

pp. 2348-2358 ◽

Author(s):

Yuhang Wang ◽

Jason A. Wallace ◽

Peter H. Koenig ◽

Jana K. Shen

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Nonionic Surfactant ◽

Implicit Solvent ◽

Generalized Born ◽

Surfactant Micelles ◽

Implicit Solvent Model ◽

Solvent Model ◽

Dynamics Simulations

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Effects of force fields for refining protein NMR structures with atomistic force fields and generalized-Born implicit solvent model

Journal of the Korean Magnetic Resonance Society ◽

10.6564/jkmrs.2014.18.1.024 ◽

2014 ◽

Vol 18 (1) ◽

pp. 24-29 ◽

Author(s):

Jun-Goo Jee

Keyword(s):

Force Fields ◽

Protein Nmr ◽

Implicit Solvent ◽

Generalized Born ◽

Implicit Solvent Model ◽

Nmr Structures ◽

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The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area

Journal of Computational Chemistry ◽

10.1002/jcc.20933 ◽

2008 ◽

Vol 29 (10) ◽

pp. 1693-1698 ◽

Author(s):

Paul Labute

Keyword(s):

Implicit Solvent ◽

Model Estimation ◽

Volume Integral ◽

Generalized Born ◽

Implicit Solvent Model ◽

Solvent Model ◽

Energy Of Hydration ◽

Atomic Surface ◽

Free Energy Of Hydration ◽

London Dispersion

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Faculty Opinions recommendation of Beta-hairpin folding simulations in atomistic detail using an implicit solvent model.

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

10.3410/f.1000071.56855 ◽

2002 ◽

Author(s):

Angel García

Keyword(s):

Implicit Solvent ◽

Implicit Solvent Model ◽

Solvent Model ◽

Beta Hairpin ◽

Folding Simulations

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Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units

Journal of Computational Chemistry ◽

10.1002/jcc.26133 ◽

2019 ◽

Vol 41 (8) ◽

pp. 830-838 ◽

Author(s):

Xiping Gong ◽

Mara Chiricotto ◽

Xiaorong Liu ◽

Erik Nordquist ◽

Michael Feig ◽

...

Keyword(s):

Graphics Processing Units ◽

Accessible Surface Area ◽

Solvent Accessible Surface Area ◽

Molecular Volume ◽

Implicit Solvent ◽

Generalized Born ◽

Solvent Model ◽

Accessible Surface ◽

Graphics Processing ◽

Solvent Accessible Surface

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Molecular Dynamics Calculation of Interaction Forces between Colloids in Aqueous Electrolyte Solutions Using an Implicit Solvent Model

KAGAKU KOGAKU RONBUNSHU ◽

10.1252/kakoronbunshu.31.295 ◽

2005 ◽

Vol 31 (5) ◽

pp. 295-300 ◽

Author(s):

Shintaro Morisada ◽

Kenji Muranishi ◽

Hiroyuki Shinto ◽

Ko Higashitani

Keyword(s):

Molecular Dynamics ◽

Aqueous Electrolyte ◽

Electrolyte Solutions ◽

Implicit Solvent ◽

Interaction Forces ◽

Implicit Solvent Model ◽

Aqueous Electrolyte Solutions ◽

Solvent Model ◽

Dynamics Calculation

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Particle-Based Implicit Solvent Model for Biosimulations: Application to Proteins and Nucleic Acids Hydration

Journal of Chemical Theory and Computation ◽

10.1021/ct0600417 ◽

2006 ◽

Vol 2 (6) ◽

pp. 1646-1656 ◽

Author(s):

Nathalie Basdevant ◽

Tap Ha-Duong ◽

Daniel Borgis

Keyword(s):

Nucleic Acids ◽

Implicit Solvent ◽

Implicit Solvent Model ◽

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Exploring large-scale phenomena in composite membranes through an efficient implicit-solvent model

Journal of Physics D Applied Physics ◽

10.1088/0022-3727/49/29/293001 ◽

2016 ◽

Vol 49 (29) ◽

pp. 293001 ◽

Author(s):

Mohamed Laradji ◽

P B Sunil Kumar ◽

Eric J Spangler

Keyword(s):

Large Scale ◽

Composite Membranes ◽

Implicit Solvent ◽

Implicit Solvent Model ◽

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All-Atom Direct Folding Simulation for Proteins Using the Accelerated Molecular Dynamics in Implicit Solvent Model

Chinese Physics Letters ◽

10.1088/0256-307x/32/11/118701 ◽

2015 ◽

Vol 32 (11) ◽

pp. 118701 ◽

Author(s):

Zong-Chao Li ◽

Li-Li Duan ◽

Guo-Qiang Feng ◽

Qing-Gang Zhang

Keyword(s):

Molecular Dynamics ◽

Implicit Solvent ◽

Implicit Solvent Model ◽

Accelerated Molecular Dynamics ◽

Folding Simulation ◽

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