Development and validation of hydrophobic molecular fields derived from the quantum mechanical IEF/PCM-MST solvation models in 3D-QSAR

2016 ◽  
Vol 37 (13) ◽  
pp. 1147-1162 ◽  
Author(s):  
Tiziana Ginex ◽  
Jordi Muñoz-Muriedas ◽  
Enric Herrero ◽  
Enric Gibert ◽  
Pietro Cozzini ◽  
...  
Keyword(s):  
3D Qsar ◽  
Quantum Mechanical ◽  
Solvation Models ◽  
Molecular Fields ◽  
Development And Validation

Quantum Mechanical Continuum Solvation Models for Ionic Liquids

2012 ◽  
Vol 116 (30) ◽  
pp. 9122-9129 ◽  
Author(s):  
Varinia S. Bernales ◽  
Aleksandr V. Marenich ◽  
Renato Contreras ◽  
Christopher J. Cramer ◽  
Donald G. Truhlar
Keyword(s):  
Ionic Liquids ◽  
Quantum Mechanical ◽  
Continuum Solvation ◽  
Solvation Models

scholarly journals Development and Validation of the Quantum Mechanical Bespoke Protein Force Field

ACS Omega ◽  
2019 ◽  
Vol 4 (11) ◽  
pp. 14537-14550 ◽  
Author(s):  
Alice E. A. Allen ◽  
Michael J. Robertson ◽  
Michael C. Payne ◽  
Daniel J. Cole
Keyword(s):  
Force Field ◽  
Quantum Mechanical ◽  
Development And Validation

Assessing the hydration free energy of a homologous series of polyols with classical and quantum mechanical solvation models

2014 ◽  
Vol 16 (33) ◽  
pp. 17863-17868 ◽  
Author(s):  
Thaciana Malaspina ◽  
Leonardo M. Abreu ◽  
Tertius L. Fonseca ◽  
Eudes Fileti
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Homologous Series ◽  
Continuum Model ◽  
Polarizable Continuum Model ◽  
Quantum Mechanical ◽  
Hydration Free Energy ◽  
Solvation Model ◽  
Solvation Models ◽  
Polarizable Continuum

Molecular dynamics (MD) and the polarizable continuum model (PCM) in combination with the SMD solvation model were used to study the hydration free energy of the homologous series of polyols, CnHn+2(OH)n (1 ≤ n ≤ 7).

scholarly journals Development and Validation of the QUBE Protein Force Field

2019 ◽  
Author(s):  
Alice Allen ◽  
Michael J. Robertson ◽  
Michael C. Payne ◽  
Daniel Cole
Keyword(s):  
Force Field ◽  
Specific Protein ◽  
Biological Molecules ◽  
Quantum Mechanical ◽  
J Coupling ◽  
Force Field Parameters ◽  
Folded Proteins ◽  
Dynamics Simulations ◽  
Complete Protein ◽  
Development And Validation

<div><div><div><p>Molecular mechanics force field parameters for macromolecules, such as proteins, are traditionally fit to reproduce experimental properties of small molecules, and thus they neglect system-specific polarization. In this paper, we introduce a complete protein force field that is designed to be compatible with the QUantum mechanical BEspoke (QUBE) force field by deriving non-bonded parameters directly from the electron density of the specific protein under study. The main backbone and sidechain protein torsional parameters are re-derived in this work by fitting to quantum mechanical dihedral scans for compatibility with QUBE non-bonded parameters. Software is provided for the preparation of QUBE input files. The accuracy of the new force field, and the derived torsional parameters, are tested by comparing the conformational preferences of a range of peptides and proteins with experimental measurements. Accurate backbone and sidechain conformations are obtained in molecular dynamics simulations of dipeptides, with NMR J coupling errors comparable to the widely-used OPLS force field. In simulations of five folded proteins, the secondary structure is generally retained and the NMR J coupling errors are similar to standard transferable force fields, although some loss of the experimental structure is observed in certain regions of the proteins. With several avenues for further development, the use of system-specific non-bonded force field parameters is a promising approach for next-generation simulations of biological molecules.</p></div></div></div>

Sign in / Sign up

Export Citation Format

Share Document