Binding Mechanism of Thrombin–Ligand Systems Investigated by a Polarized Protein-Specific Charge Force Field and Interaction Entropy Method

2019 ◽  
Vol 123 (41) ◽  
pp. 8704-8716 ◽  
Author(s):  
Susu Zhong ◽  
Kaifang Huang ◽  
Zhengrong Xiao ◽  
Xiehuang Sheng ◽  
Yuchen Li ◽  
...  
Keyword(s):  
Force Field ◽  
Entropy Method ◽  
Specific Charge ◽  
Binding Mechanism

Effect of electrostatic polarization and bridging water on CDK2–ligand binding affinities calculated using a highly efficient interaction entropy method

2017 ◽  
Vol 19 (15) ◽  
pp. 10140-10152 ◽  
Author(s):  
Lili Duan ◽  
Guoqiang Feng ◽  
Xianwei Wang ◽  
Lizhi Wang ◽  
Qinggang Zhang
Keyword(s):  
Ligand Binding ◽  
Force Field ◽  
Interaction Mechanism ◽  
Entropy Method ◽  
Binding Affinities ◽  
Specific Charge ◽  
Highly Efficient ◽  
Electrostatic Polarization

A new highly efficient interaction entropy (IE) method combined with the polarized protein-specific charge (PPC) force field is employed to investigate the interaction mechanism of CDK2–ligand binding and the effect of the bridging water.

scholarly journals Insight Into the Binding Mechanism of p53/pDIQ-MDMX/MDM2 With the Interaction Entropy Method

2019 ◽  
Vol 7 ◽  
Author(s):  
Mengxin Li ◽  
Yalong Cong ◽  
Yuchen Li ◽  
Susu Zhong ◽  
Ran Wang ◽  
...  
Keyword(s):  
Entropy Method ◽  
Binding Mechanism ◽  
Insight Into

scholarly journals Trypsin-Ligand binding affinities calculated using an effective interaction entropy method under polarized force field

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Yalong Cong ◽  
Mengxin Li ◽  
Guoqiang Feng ◽  
Yuchen Li ◽  
Xianwei Wang ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Force Field ◽  
Effective Interaction ◽  
Entropy Method ◽  
Binding Affinities

Millimetre-wave and infrared spectroscopy of Br13 CN: anharmonic force field of cyanogen bromide from spectroscopic data and ab initio calculations

1997 ◽  
Vol 90 (3) ◽  
pp. 495-497
Author(s):  
CLAUDIO ESPOSTI ◽  
FILIPPO TAMASSIA ◽  
CRISTINA PUZZARINI ◽  
RICCARDO TARRONI ◽  
ZDENEK ZELINGER
Keyword(s):  
Infrared Spectroscopy ◽  
Force Field ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Spectroscopic Data ◽  
Cyanogen Bromide ◽  
Millimetre Wave ◽  
Anharmonic Force

Molecular force field evaluation by empirical constraints

1976 ◽  
Vol 73 ◽  
pp. 1051-1057
Author(s):  
Sadao Isotani ◽  
Alain J.-P. Alix
Keyword(s):  
Force Field ◽  
Field Evaluation ◽  
Molecular Force ◽  
Molecular Force Field

Optimization of a New Reactive Force Field for Silver - Based Materials

2020 ◽  
Author(s):  
Clément Dulong ◽  
Bruno Madebène ◽  
Susanna Monti ◽  
Johannes Richardi
Keyword(s):  
Force Field ◽  
Self Assembled Monolayers ◽  
The Novel ◽  
Reactive Force ◽  
Reactive Force Field ◽  
Energetic Properties ◽  
Extended Training ◽  
Geometrical Features ◽  
Assembled Monolayers ◽  
Gold Thiolate

<div><div><div><p>A new reactive force field based on the ReaxFF formalism is effectively parametrized against an extended training set of quantum chemistry data (containing more than 120 different structures) to describe accurately silver- and silver-thiolate systems. The results obtained with this novel representation demonstrate that the novel ReaxFF paradigm is a powerful methodology to reproduce more appropriately average geometric and energetic properties of metal clusters and slabs when compared to the earlier ReaxFF parametrizations dealing with silver and gold. ReaxFF cannot describe adequately specific geometrical features such as the observed shorter distances between the under-coordinated atoms at the cluster edges. Geometric and energetic properties of thiolates adsorbed on a silver Ag20 pyramid are correctly represented by the new ReaxFF and compared with results for gold. The simulation of self-assembled monolayers of thiolates on a silver (111) surface does not indicate the formation of staples in contrast to the results for gold-thiolate systems.</p></div></div></div>

Driving Torsion Scans with Wavefront Propagation

2020 ◽  
Author(s):  
Yudong Qiu ◽  
Daniel Smith ◽  
Chaya Stern ◽  
mudong feng ◽  
Lee-Ping Wang
Keyword(s):  
Potential Energy ◽  
Force Field ◽  
Degrees Of Freedom ◽  
Computational Cost ◽  
Initial Guess ◽  
Field Development ◽  
Force Field Development ◽  
Wavefront Propagation ◽  
Open Source Software Package

<div>The parameterization of torsional / dihedral angle potential energy terms is a crucial part of developing molecular mechanics force fields.</div><div>Quantum mechanical (QM) methods are often used to provide samples of the potential energy surface (PES) for fitting the empirical parameters in these force field terms.</div><div>To ensure that the sampled molecular configurations are thermodynamically feasible, constrained QM geometry optimizations are typically carried out, which relax the orthogonal degrees of freedom while fixing the target torsion angle(s) on a grid of values.</div><div>However, the quality of results and computational cost are affected by various factors on a non-trivial PES, such as dependence on the chosen scan direction and the lack of efficient approaches to integrate results started from multiple initial guesses.</div><div>In this paper we propose a systematic and versatile workflow called \textit{TorsionDrive} to generate energy-minimized structures on a grid of torsion constraints by means of a recursive wavefront propagation algorithm, which resolves the deficiencies of conventional scanning approaches and generates higher quality QM data for force field development.</div><div>The capabilities of our method are presented for multi-dimensional scans and multiple initial guess structures, and an integration with the MolSSI QCArchive distributed computing ecosystem is described.</div><div>The method is implemented in an open-source software package that is compatible with many QM software packages and energy minimization codes.</div>

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