Publications by authors named "Edward Harder"

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Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation.
Eelke B Lenselink, Julien Louvel, Anna F Forti, Jacobus P D van Veldhoven, Henk de Vries, Thea Mulder-Krieger, Fiona M McRobb, Ana Negri, Joseph Goose, Robert Abel

ACS Omega· August 2016

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Accurate Physics-Based Prediction of Binding Affinities of RNA- and DNA-Targeting Ligands.
Ara M Abramyan, Anna Bochicchio, Chuanjie Wu, Wolfgang Damm, David R Langley, Edward Harder

J Chem Inf Model· February 2025

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CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.
Wonmuk Hwang, Steven L Austin, Arnaud Blondel, Eric D Boittier, Stefan Boresch, Edward D Harder

J Phys Chem B· October 2024

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A Method for Treating Significant Conformational Changes in Alchemical Free Energy Simulations of Protein-Ligand Binding.
Junzhuo Liao, Alina P Sergeeva, Edward D Harder, Lingle Wang, Jared M Sampson

J Chem Theory Comput· October 2024

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The maximal and current accuracy of rigorous protein-ligand binding free energy calculations.
Gregory A Ross, Chao Lu, Guido Scarabelli, Steven K Albanese, Evelyne Houang, Edward D Harder

Commun Chem· October 2023

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Reliable and Accurate Prediction of Single-Residue p Values through Free Energy Perturbation Calculations.
Dilek Coskun, Wei Chen, Anthony J Clark, Chao Lu, Edward D Harder

J Chem Theory Comput· December 2022

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Transferable Neural Network Potential Energy Surfaces for Closed-Shell Organic Molecules: Extension to Ions.
Leif D Jacobson, James M Stevenson, Farhad Ramezanghorbani, Delaram Ghoreishi, Karl Leswing, Edward D Harder

J Chem Theory Comput· April 2022

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OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space.
Chao Lu, Chuanjie Wu, Delaram Ghoreishi, Wei Chen, Lingle Wang, Edward D Harder

J Chem Theory Comput· July 2021

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Advancing Free-Energy Calculations of Metalloenzymes in Drug Discovery via Implementation of LFMM Potentials.
Steven Dajnowicz, Delaram Ghoreishi, Kalyan Modugula, Wolfgang Damm, Edward D Harder

J Chem Theory Comput· November 2020

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Enhancing Water Sampling in Free Energy Calculations with Grand Canonical Monte Carlo.
Gregory A Ross, Ellery Russell, Yuqing Deng, Chao Lu, Edward D Harder

J Chem Theory Comput· October 2020

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Toward Atomistic Modeling of Irreversible Covalent Inhibitor Binding Kinetics.
Haoyu S Yu, Cen Gao, Dmitry Lupyan, Yujie Wu, Takayuki Kimura, Edward Harder

J Chem Inf Model· September 2019

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OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules.
Katarina Roos, Chuanjie Wu, Wolfgang Damm, Mark Reboul, James M Stevenson, Edward D Harder

J Chem Theory Comput· March 2019

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Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator.
Fang-Yu Lin, Pedro E M Lopes, Edward Harder, Benoît Roux, Alexander D MacKerell

J Chem Inf Model· May 2018

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High Energy Density in Azobenzene-based Materials for Photo-Thermal Batteries via Controlled Polymer Architecture and Polymer-Solvent Interactions.
Seung Pyo Jeong, Lawrence A Renna, Connor J Boyle, Hyunwook S Kwak, Edward Harder

Sci Rep· December 2017

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Advancing Drug Discovery through Enhanced Free Energy Calculations.
Robert Abel, Lingle Wang, Edward D Harder, B J Berne, Richard A Friesner

Acc Chem Res· July 2017

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OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.
Edward Harder, Wolfgang Damm, Jon Maple, Chuanjie Wu, Mark Reboul

J Chem Theory Comput· January 2016

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How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.
Joseph W Kaus, Edward Harder, Teng Lin, Robert Abel, J Andrew McCammon

J Chem Theory Comput· June 2015

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Docking covalent inhibitors: a parameter free approach to pose prediction and scoring.
Kai Zhu, Kenneth W Borrelli, Jeremy R Greenwood, Tyler Day, Robert Abel, Edward Harder

J Chem Inf Model· July 2014

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A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids.
Janamejaya Chowdhary, Edward Harder, Pedro E M Lopes, Lei Huang, Alexander D MacKerell

J Phys Chem B· August 2013

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Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field.
Devleena Shivakumar, Edward Harder, Wolfgang Damm, Richard A Friesner, Woody Sherman

J Chem Theory Comput· August 2012

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Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field.
Haibo Yu, Troy W Whitfield, Edward Harder, Guillaume Lamoureux, Igor Vorobyov

J Chem Theory Comput· January 2010

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Molecular dynamics study of a polymeric reverse osmosis membrane.
Edward Harder, D Eric Walters, Yaroslav D Bodnar, Ron S Faibish, Benoît Roux

J Phys Chem B· July 2009

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Many-body polarization effects and the membrane dipole potential.
Edward Harder, Alexander D Mackerell, Benoît Roux

J Am Chem Soc· March 2009

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On the origin of the electrostatic potential difference at a liquid-vacuum interface.
Edward Harder, Benoît Roux

J Chem Phys· December 2008

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Understanding the dielectric properties of liquid amides from a polarizable force field.
Edward Harder, Victor M Anisimov, Troy Whitfield, Alexander D MacKerell, Benoît Roux

J Phys Chem B· March 2008

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