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Edward D. Harder

AddressChicago IL 60637
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Yu HS, Gao C, Lupyan D, Wu Y, Kimura T, Wu C, Jacobson L, Harder E, Abel R, Wang L. Toward Atomistic Modeling of Irreversible Covalent Inhibitor Binding Kinetics. J Chem Inf Model. 2019 Sep 23; 59(9):3955-3967. PMID: 31425654.
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    2. 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. J Chem Theory Comput. 2019 Mar 12; 15(3):1863-1874. PMID: 30768902.
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    3. Lin FY, Lopes PEM, Harder E, Roux B, MacKerell AD. Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator. J Chem Inf Model. 2018 05 29; 58(5):993-1004. PMID: 29624370.
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    4. Jeong SP, Renna LA, Boyle CJ, Kwak HS, Harder E, Damm W, Venkataraman D. High Energy Density in Azobenzene-based Materials for Photo-Thermal Batteries via Controlled Polymer Architecture and Polymer-Solvent Interactions. Sci Rep. 2017 12 19; 7(1):17773. PMID: 29259213.
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    5. Abel R, Wang L, Harder ED, Berne BJ, Friesner RA. Advancing Drug Discovery through Enhanced Free Energy Calculations. Acc Chem Res. 2017 07 18; 50(7):1625-1632. PMID: 28677954.
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    6. 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, Beuming T. Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation. ACS Omega. 2016 Aug 31; 1(2):293-304. PMID: 30023478.
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    7. Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti DS, Krilov G, Jorgensen WL, Abel R, Friesner RA. OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins. J Chem Theory Comput. 2016 Jan 12; 12(1):281-96. PMID: 26584231.
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    8. 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. J Chem Theory Comput. 2015 Jun 09; 11(6):2670-9. PMID: 26085821.
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    9. 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, Damm W, Harder E, Sherman W, Brewer M, Wester R, Murcko M, Frye L, Farid R, Lin T, Mobley DL, Jorgensen WL, Berne BJ, Friesner RA, Abel R. 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. J Am Chem Soc. 2015 Feb 25; 137(7):2695-703. PMID: 25625324.
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    10. 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. J Chem Inf Model. 2014 Jul 28; 54(7):1932-40. PMID: 24916536.
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    11. 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. J Phys Chem B. 2013 Aug 08; 117(31):9142-60. PMID: 23841725.
      View in: PubMed
    12. Huang EY, Leone VA, Devkota S, Wang Y, Brady MJ, Chang EB. Composition of dietary fat source shapes gut microbiota architecture and alters host inflammatory mediators in mouse adipose tissue. JPEN J Parenter Enteral Nutr. 2013 Nov; 37(6):746-54. PMID: 23639897.
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    13. 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. J Chem Theory Comput. 2012 Aug 14; 8(8):2553-8. PMID: 26592101.
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    14. 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. J Chem Theory Comput. 2010; 6(3):774-786. PMID: 20300554.
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    15. Harder E, Walters DE, Bodnar YD, Faibish RS, Roux B. Molecular dynamics study of a polymeric reverse osmosis membrane. J Phys Chem B. 2009 Jul 30; 113(30):10177-82. PMID: 19586002.
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    16. Harder E, Mackerell AD, Roux B. Many-body polarization effects and the membrane dipole potential. J Am Chem Soc. 2009 Mar 04; 131(8):2760-1. PMID: 19199514.
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    17. Harder E, Roux B. On the origin of the electrostatic potential difference at a liquid-vacuum interface. J Chem Phys. 2008 Dec 21; 129(23):234706. PMID: 19102551.
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    18. Harder E, Anisimov VM, Whitfield T, MacKerell AD, Roux B. Understanding the dielectric properties of liquid amides from a polarizable force field. J Phys Chem B. 2008 Mar 20; 112(11):3509-21. PMID: 18302362.
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    19. 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. J Chem Theory Comput. 2007; 3(6):2068-2082. PMID: 21785577.
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    20. 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. J Chem Theory Comput. 2006 Nov; 2(6):1587-97. PMID: 26627029.
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    21. 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. J Phys Chem B. 2005 Sep 01; 109(34):16529-38. PMID: 16853101.
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    22. Harder E, Eaves JD, Tokmakoff A, Berne BJ. Polarizable molecules in the vibrational spectroscopy of water. Proc Natl Acad Sci U S A. 2005 Aug 16; 102(33):11611-6. PMID: 16081533.
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    23. Liu P, Harder E, Berne BJ. Hydrogen-bond dynamics in the air-water interface. J Phys Chem B. 2005 Feb 24; 109(7):2949-55. PMID: 16851308.
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    24. 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. J Chem Theory Comput. 2005 Jan; 1(1):169-80. PMID: 26641127.
      View in: PubMed
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