scholarly journals Using polarizable POSSIM force field and fuzzy-border continuum solvent model to calculate pKashifts of protein residues

2016 ◽  
Vol 38 (2) ◽  
pp. 65-80 ◽  
Author(s):  
Ity Sharma ◽  
George A. Kaminski
Keyword(s):  
Force Field ◽  
Protein Residues ◽  
Continuum Solvent Model ◽  
Solvent Model

Hydration Free Energies of Organic Molecules in the FreeSolv Database Calculated with Polarized Atom In Molecules Atomic Charges and the GAFF Force Field.

2018 ◽  
Author(s):  
Maximiliano Riquelme ◽  
Alejandro Lara ◽  
David L. Mobley ◽  
Toon Vestraelen ◽  
Adelio R Matamala ◽  
...  
Keyword(s):  
Force Field ◽  
Functional Groups ◽  
Electrostatic Interactions ◽  
Organic Molecules ◽  
Force Fields ◽  
Chemical Elements ◽  
Atomic Charges ◽  
Free Energies ◽  
Molecular Systems ◽  
Solvent Model

<div>Computer simulations of bio-molecular systems often use force fields, which are combinations of simple empirical atom-based functions to describe the molecular interactions. Even though polarizable force fields give a more detailed description of intermolecular interactions, nonpolarizable force fields, developed several decades ago, are often still preferred because of their reduced computation cost. Electrostatic interactions play a major role in bio-molecular systems and are therein described by atomic point charges.</div><div>In this work, we address the performance of different atomic charges to reproduce experimental hydration free energies in the FreeSolv database in combination with the GAFF force field. Atomic charges were calculated by two atoms-in-molecules approaches, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS). To account for polarization effects, the charges were derived from the solute's electron density computed with an implicit solvent model and the energy required to polarize the solute was added to the free energy cycle. The calculated hydration free energies were analyzed with an error model, revealing systematic errors associated with specific functional groups or chemical elements. The best agreement with the experimental data is observed for the MBIS atomic charge method, including the solvent polarization, with a root mean square error of 2.0 kcal mol<sup>-1</sup> for the 613 organic molecules studied. The largest deviation was observed for phosphor-containing molecules and the molecules with amide, ester and amine functional groups.</div>

Molecular dynamics of cryptophane and its complexes with tetramethylammonium and neopentane using a continuum solvent model

1999 ◽  
Vol 20 (9) ◽  
pp. 956-970 ◽  
Author(s):  
Michael J. Potter ◽  
Paul D. Kirchhoff ◽  
Heather A. Carlson ◽  
J. Andrew McCammon
Keyword(s):  
Molecular Dynamics ◽  
Continuum Solvent Model ◽  
Solvent Model

Improving ligand 3D shape similarity-based pose prediction with a continuum solvent model

2019 ◽  
Vol 33 (12) ◽  
pp. 1045-1055 ◽  
Author(s):  
Ashutosh Kumar ◽  
Kam Y. J. Zhang
Keyword(s):  
Shape Similarity ◽  
Pose Prediction ◽  
3D Shape ◽  
Continuum Solvent Model ◽  
Solvent Model ◽  
Ligand 3D Shape Similarity

A continuum solvent model of ion–ion interactions in water

2014 ◽  
Vol 16 (40) ◽  
pp. 22014-22027 ◽  
Author(s):  
Timothy T. Duignan ◽  
Drew F. Parsons ◽  
Barry W. Ninham
Keyword(s):  
Ion Interactions ◽  
Continuum Solvent Model ◽  
Solvent Model

We present a continuum solvent model of ion–ion interactions in water that reproduces activities with only two fitted parameters.

scholarly journals Continuum Solvent Model Calculations of Alamethicin-Membrane Interactions: Thermodynamic Aspects

2000 ◽  
Vol 78 (2) ◽  
pp. 571-583 ◽  
Author(s):  
Amit Kessel ◽  
David S. Cafiso ◽  
Nir Ben-Tal
Keyword(s):  
Membrane Interactions ◽  
Model Calculations ◽  
Continuum Solvent Model ◽  
Solvent Model

Calculating solvation energies by means of a fluctuating charge model combined with continuum solvent model

2011 ◽  
Vol 134 (19) ◽  
pp. 194115 ◽  
Author(s):  
Dong-Xia Zhao ◽  
Ling Yu ◽  
Li-Dong Gong ◽  
Cui Liu ◽  
Zhong-Zhi Yang
Keyword(s):  
Continuum Solvent Model ◽  
Charge Model ◽  
Solvent Model ◽  
Solvation Energies

A Continuum Solvent Model of the Multipolar Dispersion Solvation Energy

2013 ◽  
Vol 117 (32) ◽  
pp. 9412-9420 ◽  
Author(s):  
Timothy T. Duignan ◽  
Drew F. Parsons ◽  
Barry W. Ninham
Keyword(s):  
Solvation Energy ◽  
Continuum Solvent Model ◽  
Solvent Model
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