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Edward Daniel Harder, Ph.D. - Publications

Affiliations: 
2004 Columbia University, New York, NY 
Area:
Theory of liquids, molecular dynamics and Monte Carlo simulations of condensed matter
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38 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Ross GA, Lu C, Scarabelli G, Albanese SK, Houang E, Abel R, Harder ED, Wang L. The maximal and current accuracy of rigorous protein-ligand binding free energy calculations. Communications Chemistry. 6: 222. PMID 37838760 DOI: 10.1038/s42004-023-01019-9  0.725
2022 Coskun D, Chen W, Clark AJ, Lu C, Harder ED, Wang L, Friesner RA, Miller EB. Reliable and Accurate Prediction of Single-Residue p Values through Free Energy Perturbation Calculations. Journal of Chemical Theory and Computation. PMID 36384001 DOI: 10.1021/acs.jctc.2c00954  0.664
2022 Jacobson LD, Stevenson JM, Ramezanghorbani F, Ghoreishi D, Leswing K, Harder ED, Abel R. Transferable Neural Network Potential Energy Surfaces for Closed-Shell Organic Molecules: Extension to Ions. Journal of Chemical Theory and Computation. PMID 35290063 DOI: 10.1021/acs.jctc.1c00821  0.326
2021 Lu C, Wu C, Ghoreishi D, Chen W, Wang L, Damm W, Ross GA, Dahlgren MK, Russell E, Von Bargen CD, Abel R, Friesner RA, Harder ED. OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space. Journal of Chemical Theory and Computation. PMID 34096718 DOI: 10.1021/acs.jctc.1c00302  0.715
2020 Ross GA, Russell E, Deng Y, Lu C, Harder ED, Abel R, Wang L. Enhancing water sampling in free energy calculations with grand canonical Monte Carlo. Journal of Chemical Theory and Computation. PMID 32955877 DOI: 10.1021/Acs.Jctc.0C00660  0.73
2020 Dajnowicz S, Ghoreishi D, Modugula K, Damm W, Harder ED, Abel R, Wang L, Yu HS. Advancing Free Energy Calculations of Metalloenzyme in Drug Discovery via Implementation of LFMM Potentials. Journal of Chemical Theory and Computation. PMID 32910652 DOI: 10.1021/Acs.Jctc.0C00615  0.728
2019 Yu HS, Gao C, Lupyan D, Wu Y, Kimura T, Wu C, Jacobson L, Harder ED, Abel R, Wang L. Towards Atomistic Modelling of Irreversible Covalent Inhibitor Binding Kinetics. Journal of Chemical Information and Modeling. PMID 31425654 DOI: 10.1021/Acs.Jcim.9B00268  0.704
2019 Roos K, Wu C, Damm W, Reboul M, Stevenson JM, Lu C, Dahlgren MK, Mondal S, Chen W, Wang L, Abel R, Friesner RA, Harder ED. OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules. Journal of Chemical Theory and Computation. PMID 30768902 DOI: 10.1021/Acs.Jctc.8B01026  0.738
2018 Lin FY, Lopes PE, Harder ED, Roux B, MacKerell AD. Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator. Journal of Chemical Information and Modeling. PMID 29624370 DOI: 10.1021/Acs.Jcim.8B00132  0.463
2017 Abel R, Wang L, Harder ED, Berne BJ, Friesner RA. Advancing Drug Discovery through Enhanced Free Energy Calculations. Accounts of Chemical Research. PMID 28677954 DOI: 10.1021/Acs.Accounts.7B00083  0.763
2016 Lenselink EB, Louvel J, Forti AF, van Veldhoven JPD, de Vries H, Mulder-Krieger T, McRobb FM, Negri A, Goose J, Abel R, van Vlijmen HWT, Wang L, Harder E, Sherman W, IJzerman AP, et al. Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation. Acs Omega. 1: 293-304. PMID 30023478 DOI: 10.1021/acsomega.6b00086  0.706
2015 Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti D, Krilov G, Jorgensen WL, Abel R, et al. OPLS3: a force field providing broad coverage of drug-like small molecules and proteins. Journal of Chemical Theory and Computation. PMID 26584231 DOI: 10.1021/Acs.Jctc.5B00864  0.769
2015 Kaus JW, Harder E, Lin T, Abel R, McCammon JA, Wang L. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations. Journal of Chemical Theory and Computation. 11: 2670-9. PMID 26085821 DOI: 10.1021/Acs.Jctc.5B00214  0.731
2015 Wang L, Wu Y, Deng Y, Kim B, Pierce L, Krilov G, Lupyan D, Robinson S, Dahlgren MK, Greenwood J, Romero DL, Masse C, Knight JL, Steinbrecher T, Beuming T, ... ... Harder E, et al. Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field. Journal of the American Chemical Society. 137: 2695-703. PMID 25625324 DOI: 10.1021/Ja512751Q  0.766
2014 Zhu K, Borrelli KW, Greenwood JR, Day T, Abel R, Farid RS, Harder E. Docking covalent inhibitors: a parameter free approach to pose prediction and scoring. Journal of Chemical Information and Modeling. 54: 1932-40. PMID 24916536 DOI: 10.1021/Ci500118S  0.418
2014 Roux B, Li H, Chowdhary J, Harder E, Lopes PE, Huang L, MacKerell AD. Ion Channel Simulation with Explicit Solvent and Lipid Membrane Based on the Drude Polarizable Force Field Biophysical Journal. 106: 44a. DOI: 10.1016/J.Bpj.2013.11.319  0.402
2013 Chowdhary J, Harder E, Lopes PE, Huang L, MacKerell AD, Roux B. A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids. The Journal of Physical Chemistry. B. 117: 9142-60. PMID 23841725 DOI: 10.1021/Jp402860E  0.374
2013 Chowdhary J, Li H, Harder E, Lopes P, MacKerell A, Roux B. Drude Model Based Polarizable Force Field for Lipids Biophysical Journal. 104: 31a. DOI: 10.1016/J.Bpj.2012.11.210  0.394
2013 Bochevarov AD, Harder E, Hughes TF, Greenwood JR, Braden DA, Philipp DM, Rinaldo D, Halls MD, Zhang J, Friesner RA. Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences International Journal of Quantum Chemistry. 113: 2110-2142. DOI: 10.1002/Qua.24481  0.36
2012 Shivakumar D, Harder E, Damm W, Friesner RA, Sherman W. Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field. Journal of Chemical Theory and Computation. 8: 2553-8. PMID 26592101 DOI: 10.1021/Ct300203W  0.502
2012 Shivakumar D, Harder E, Damm W, Friesner RA, Sherman W. Improving the prediction of absolute solvation free energies using the next generation opls force field Journal of Chemical Theory and Computation. 8: 2553-2558. DOI: 10.1021/ct300203w  0.34
2011 Luo Y, Harder E, Faibish RS, Roux B. Computer simulations of water flux and salt permeability of the reverse osmosis FT-30 aromatic polyamide membrane Journal of Membrane Science. 384: 1-9. DOI: 10.1016/J.Memsci.2011.08.057  0.326
2010 Yu H, Whitfield TW, Harder E, Lamoureux G, Vorobyov I, Anisimov VM, Mackerell AD, Roux B. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. Journal of Chemical Theory and Computation. 6: 774-786. PMID 20300554 DOI: 10.1021/Ct900576A  0.312
2010 Harder E, Roux B, MacKerell AD. Molecular Dynamics Simulation of Phospholipid Bilayers and Monolayers Using a Polarizable Force Field Biophysical Journal. 98: 10a. DOI: 10.1016/J.Bpj.2009.12.061  0.376
2009 Harder E, Mackerell AD, Roux B. Many-body polarization effects and the membrane dipole potential. Journal of the American Chemical Society. 131: 2760-1. PMID 19199514 DOI: 10.1021/Ja806825G  0.339
2009 Harder E, Roux B. On the origin of the electrostatic potential difference at a liquid-vacuum interface. The Journal of Chemical Physics. 129: 234706. PMID 19102551 DOI: 10.1063/1.3027513  0.37
2008 Harder E, Anisimov VM, Whitfield T, MacKerell AD, Roux B. Understanding the dielectric properties of liquid amides from a polarizable force field Journal of Physical Chemistry B. 112: 3509-3521. PMID 18302362 DOI: 10.1021/Jp709729D  0.358
2007 Whitfield TW, Varma S, Harder E, Lamoureux G, Rempe SB, Roux B. A theoretical study of aqueous solvation of K comparing ab initio, polarizable, and fixed-charge models. Journal of Chemical Theory and Computation. 3: 2068-2082. PMID 21785577 DOI: 10.1021/Ct700172B  0.417
2006 Harder E, Anisimov VM, Vorobyov IV, Lopes PE, Noskov SY, MacKerell AD, Roux B. Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator. Journal of Chemical Theory and Computation. 2: 1587-97. PMID 26627029 DOI: 10.1021/Ct600180X  0.402
2006 Lamoureux G, Harder E, Vorobyov IV, Roux B, MacKerell AD. A polarizable model of water for molecular dynamics simulations of biomolecules Chemical Physics Letters. 418: 245-249. DOI: 10.1016/J.Cplett.2005.10.135  0.4
2005 Harder E, Kim B, Friesner RA, Berne BJ. Efficient Simulation Method for Polarizable Protein Force Fields:  Application to the Simulation of BPTI in Liquid Water. Journal of Chemical Theory and Computation. 1: 169-80. PMID 26641127 DOI: 10.1021/Ct049914S  0.618
2005 Kim B, Young T, Harder E, Friesner RA, Berne BJ. Structure and dynamics of the solvation of bovine pancreatic trypsin inhibitor in explicit water: a comparative study of the effects of solvent and protein polarizability. The Journal of Physical Chemistry. B. 109: 16529-38. PMID 16853101 DOI: 10.1021/Jp051569V  0.562
2005 Liu P, Harder E, Berne BJ. Hydrogen-bond dynamics in the air-water interface. The Journal of Physical Chemistry. B. 109: 2949-55. PMID 16851308 DOI: 10.1021/Jp046807L  0.579
2005 Harder E, Eaves JD, Tokmakoff A, Berne BJ. Polarizable molecules in the vibrational spectroscopy of water. Proceedings of the National Academy of Sciences of the United States of America. 102: 11611-6. PMID 16081533 DOI: 10.1073/Pnas.0505206102  0.563
2005 Harder E, Kim B, Friesner RA, Berne BJ. Efficient simulation method for polarizable protein force fields: Application to the simulation of BPTI in liquid water Journal of Chemical Theory and Computation. 1: 169-180. DOI: 10.1021/ct049914s  0.525
2004 Liu P, Harder E, Berne BJ. On the calculation of diffusion coefficients in confined fluids and interfaces with an application to the liquid-vapor interface of water Journal of Physical Chemistry B. 108: 6595-6602. DOI: 10.1021/Jp0375057  0.596
2004 Liu P, Harder E, Berne BJ. On the Calculation of Diffusion Coefficients in Confined Fluids and Interfaces with an Application to the Liquid−Vapor Interface of Water† The Journal of Physical Chemistry B. 108: 6595-6602. DOI: 10.1021/jp0375057  0.413
2001 Zhou R, Harder E, Xu H, Berne BJ. Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems Journal of Chemical Physics. 115: 2348-2358. DOI: 10.1063/1.1385159  0.727
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