Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field

Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical Drude Oscillator Force Field

(2022) Anmol Kumar et al.   Journal of Chemical Theory and Computation

Multipolar electrostatics for hairpin and pseudoknots in RNA : Improving the accuracy of force field potential energy function

(2021) Yongna Yuan et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

INDEEDopt: a deep learning-based ReaxFF parameterization framework

(2021) Mert Y. Sengul et al.   npj Computational Materials

Machine Learning Directed Optimization of Classical Molecular Modeling Force Fields

(2021) Bridgette J. Befort et al.   Journal of Chemical Information and Modeling

Benchmark Force Fields for the Molecular Dynamic Simulation of G-Quadruplexes

(2021) Na Li et al.   MOLECULES

Global Optimization of the Lennard-Jones Parameters for the Drude Polarizable Force Field

(2021) Chetan R. Rupakheti et al.   Journal of Chemical Theory and Computation

Investigating Cryptic Binding Sites by Molecular Dynamics Simulations

(2020) Antonija Kuzmanic et al.   ACCOUNTS OF CHEMICAL RESEARCH

Data-Driven Mapping of Gas-Phase Quantum Calculations to General Force Field Lennard-Jones Parameters

(2020) Sophie M. Kantonen et al.   Journal of Chemical Theory and Computation

Dynamic protein interfaces and conformational landscapes of membrane protein complexes

(2020) Shalmali A Kharche et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides

(2020) Abhishek A. Kognole et al.   JOURNAL OF MOLECULAR MODELING

How Much Dispersion Energy Is Included in the Multiconfigurational Interaction Energy?

(2020) Michał Hapka et al.   Journal of Chemical Theory and Computation

Toward Prediction of Electrostatic Parameters for Force Fields That Explicitly Treat Electronic Polarization

(2019) Esther Heid et al.   Journal of Chemical Theory and Computation

Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields

(2019) Dmitry Bedrov et al.   CHEMICAL REVIEWS

FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules

(2019) Anmol Kumar et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Conformational landscapes of membrane proteins delineated by enhanced sampling molecular dynamics simulations

(2018) Tyler J. Harpole et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Laboratory evolution of protein conformational dynamics

(2018) Eleanor C Campbell et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Folding free energy landscapes of β-sheets with non-polarizable and polarizable CHARMM force fields

(2018) Anthony J. Hazel et al.   JOURNAL OF CHEMICAL PHYSICS

Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator

(2018) Fang-Yu Lin et al.   Journal of Chemical Theory and Computation

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids

(2018) Changsheng Zhang et al.   Journal of Chemical Theory and Computation

Optimized Lennard-Jones Parameters for Druglike Small Molecules

(2018) Eliot Boulanger et al.   Journal of Chemical Theory and Computation

Improved Modeling of Halogenated Ligand–Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields

(2018) Fang-Yu Lin et al.   Journal of Chemical Information and Modeling

Escaping Atom Types in Force Fields Using Direct Chemical Perception

(2018) David L. Mobley et al.   Journal of Chemical Theory and Computation

Higher Accuracy Achieved in the Simulations of Protein Structure Refinement, Protein Folding, and Intrinsically Disordered Proteins Using Polarizable Force Fields

(2018) Anhui Wang et al.   Journal of Physical Chemistry Letters

Experimental accuracy in protein structure refinement via molecular dynamics simulations

(2018) Lim Heo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA

(2017) Justin A. Lemkul et al.   Journal of Chemical Theory and Computation

Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids

(2017) Hui Li et al.   Journal of Chemical Theory and Computation

Quantitative Characterization of the Binding and Unbinding of Millimolar Drug Fragments with Molecular Dynamics Simulations

(2017) Albert C. Pan et al.   Journal of Chemical Theory and Computation

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

(2016) Justin A. Lemkul et al.   CHEMICAL REVIEWS

A polarizable, charge transfer model of water using the drude oscillator

(2016) Steven W. Rick   JOURNAL OF COMPUTATIONAL CHEMISTRY

Balancing the Interactions of Mg2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model

(2016) Justin A. Lemkul et al.   JOURNAL OF PHYSICAL CHEMISTRY B

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design

(2015) K. Vanommeslaeghe et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Charge Transfer Models of Zinc and Magnesium in Water

(2015) Marielle Soniat et al.   Journal of Chemical Theory and Computation

Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field

(2015) Hui Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Deep learning

(2015) Yann LeCun et al.   NATURE

van der Waals dispersion interactions in molecular materials: beyond pairwise additivity

(2015) Anthony M. Reilly et al.   Chemical Science

Understanding Molecular Crystals with Dispersion-Inclusive Density Functional Theory: Pairwise Corrections and Beyond

(2014) Leeor Kronik et al.   ACCOUNTS OF CHEMICAL RESEARCH

Beyond pairwise additivity in London dispersion interactions

(2014) John F. Dobson   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Solvation of Hydrogen Sulfide in Liquid Water and at the Water–Vapor Interface Using a Polarizable Force Field

(2014) Saleh Riahi et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field

(2014) Alexey Savelyev et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Induced Polarization Influences the Fundamental Forces in DNA Base Flipping

(2014) Justin A. Lemkul et al.   Journal of Physical Chemistry Letters

Matching of Additive and Polarizable Force Fields for Multiscale Condensed Phase Simulations

(2013) Christopher M. Baker et al.   Journal of Chemical Theory and Computation

Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins

(2013) Yue Shi et al.   Journal of Chemical Theory and Computation

A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids

(2013) Janamejaya Chowdhary et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

(2012) K. Vanommeslaeghe et al.   Journal of Chemical Information and Modeling

Binding structures of tri-N-acetyl-β-glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field

(2012) Yang Zhong et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Recent applications and developments of charge equilibration force fields for modeling dynamical charges in classical molecular dynamics simulations

(2012) Brad A. Bauer et al.   THEORETICAL CHEMISTRY ACCOUNTS

Psi4: an open-source ab initio electronic structure program

(2011) Justin M. Turney et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field

(2010) Haibo Yu et al.   Journal of Chemical Theory and Computation

Polarizable empirical force field for sulfur-containing compounds based on the classical Drude oscillator model

(2010) Xiao Zhu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD

(2010) Wei Jiang et al.   Journal of Physical Chemistry Letters

Atomic-Level Characterization of the Structural Dynamics of Proteins

(2010) D. E. Shaw et al.   SCIENCE

Polarizable Simulations with Second-Order Interaction Model—Force Field and Software for Fast Polarizable Calculations: Parameters for Small Model Systems and Free Energy Calculations

(2009) George A. Kaminski et al.   Journal of Chemical Theory and Computation

Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers

(2009) Christopher M. Baker et al.   JOURNAL OF MOLECULAR MODELING

Development of a Nonlinear Classical Polarization Model for Liquid Water and Aqueous Solutions: COS/D†

(2009) Anna-Pitschna E. Kunz et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Exploring Ion Permeation Energetics in Gramicidin A Using Polarizable Charge Equilibration Force Fields

(2009) Sandeep Patel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Many-Body Polarization Effects and the Membrane Dipole Potential

(2009) Edward Harder et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator

(2008) Pedro E. M. Lopes et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Understanding the Dielectric Properties of Liquid Amides from a Polarizable Force Field

(2008) Edward Harder et al.   JOURNAL OF PHYSICAL CHEMISTRY B