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Edward D. Harder

Title
InstitutionUniversity of Chicago
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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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Abramyan AM, Bochicchio A, Wu C, Damm W, Langley DR, Shivakumar D, Lupyan D, Wang L, Harder E, Oloo EO. Accurate Physics-Based Prediction of Binding Affinities of RNA- and DNA-Targeting Ligands. J Chem Inf Model. 2025 Feb 10; 65(3):1392-1403. PMID: 39883536.
      Citations:    Fields:    
    2. Liao J, Sergeeva AP, Harder ED, Wang L, Sampson JM, Honig B, Friesner RA. A Method for Treating Significant Conformational Changes in Alchemical Free Energy Simulations of Protein-Ligand Binding. J Chem Theory Comput. 2024 Oct 08; 20(19):8609-8623. PMID: 39331379; PMCID: PMC11513859.
      Citations: 1     Fields:    Translation:Cells
    3. Hwang W, Austin SL, Blondel A, Boittier ED, Boresch S, Buck M, Buckner J, Caflisch A, Chang HT, Cheng X, Choi YK, Chu JW, Crowley MF, Cui Q, Damjanovic A, Deng Y, Devereux M, Ding X, Feig MF, Gao J, Glowacki DR, Gonzales JE, Hamaneh MB, Harder ED, Hayes RL, Huang J, Huang Y, Hudson PS, Im W, Islam SM, Jiang W, Jones MR, Käser S, Kearns FL, Kern NR, Klauda JB, Lazaridis T, Lee J, Lemkul JA, Liu X, Luo Y, MacKerell AD, Major DT, Meuwly M, Nam K, Nilsson L, Ovchinnikov V, Paci E, Park S, Pastor RW, Pittman AR, Post CB, Prasad S, Pu J, Qi Y, Rathinavelan T, Roe DR, Roux B, Rowley CN, Shen J, Simmonett AC, Sodt AJ, Töpfer K, Upadhyay M, van der Vaart A, Vazquez-Salazar LI, Venable RM, Warrensford LC, Woodcock HL, Wu Y, Brooks CL, Brooks BR, Karplus M. CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. J Phys Chem B. 2024 Oct 17; 128(41):9976-10042. PMID: 39303207; PMCID: PMC11492285.
      Citations: 9     Fields:    Translation:Cells
    4. 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. Commun Chem. 2023 Oct 14; 6(1):222. PMID: 37838760; PMCID: PMC10576784.
      Citations: 30     
    5. Friesner RA, Coskun D, Chen W, Clark AJ, Lu C, Harder ED, Wang L, Miller EB. Reliable and Accurate Prediction of Single-Residue pKa Values through Free Energy Perturbation Calculations. J Chem Theory Comput. 2022 Dec 13; 18(12):7193-7204. PMID: 36384001.
      Citations: 9     Fields:    
    6. 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. J Chem Theory Comput. 2022 Apr 12; 18(4):2354-2366. PMID: 35290063.
      Citations: 7     Fields:    Translation:Cells
    7. 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. J Chem Theory Comput. 2021 Jul 13; 17(7):4291-4300. PMID: 34096718.
      Citations: 453     Fields:    
    8. Dajnowicz S, Ghoreishi D, Modugula K, Damm W, Harder ED, Abel R, Wang L, Yu HS. Advancing Free-Energy Calculations of Metalloenzymes in Drug Discovery via Implementation of LFMM Potentials. J Chem Theory Comput. 2020 Nov 10; 16(11):6926-6937. PMID: 32910652.
      Citations: 2     Fields:    Translation:Cells
    9. 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. J Chem Theory Comput. 2020 Oct 13; 16(10):6061-6076. PMID: 32955877.
      Citations: 31     Fields:    
    10. 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 09 23; 59(9):3955-3967. PMID: 31425654.
      Citations: 12     Fields:    Translation:Cells
    11. 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.
      Citations: 415     Fields:    Translation:HumansCells
    12. Lin FY, Lopes PEM, Harder E, MacKerell AD, Roux B. 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; PMCID: PMC5975207.
      Citations: 24     Fields:    Translation:Cells
    13. Jeong SP, Renna LA, Boyle CJ, Venkataraman D, Kwak HS, Harder E, Damm W. 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; PMCID: PMC5736555.
      Citations: 5     Fields:    
    14. Berne BJ, Friesner RA, Abel R, Wang L, Harder ED. Advancing Drug Discovery through Enhanced Free Energy Calculations. Acc Chem Res. 2017 07 18; 50(7):1625-1632. PMID: 28677954.
      Citations: 117     Fields:    Translation:Cells
    15. Lenselink EB, Louvel J, Forti AF, van Veldhoven JPD, de Vries H, Mulder-Krieger T, van Vlijmen HWT, IJzerman AP, McRobb FM, Negri A, Goose J, Abel R, Wang L, Harder E, Sherman W, Beuming T. Predicting Binding Affinities for GPCR Ligands Using Free-Energy Perturbation. ACS Omega. 2016 Aug 31; 1(2):293-304. PMID: 30023478; PMCID: PMC6044636.
      Citations: 50     
    16. 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.
      Citations: 984     Fields:    Translation:Cells
    17. Harder E, Lin T, Abel R, McCammon JA, Wang L, Kaus JW. 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; PMCID: PMC4462751.
      Citations: 24     Fields:    Translation:Cells
    18. 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, Wang L. 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.
      Citations: 452     Fields:    Translation:Cells
    19. 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.
      Citations: 168     Fields:    Translation:Cells
    20. 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; PMCID: PMC3799809.
      Citations: 80     Fields:    Translation:Cells
    21. 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; PMCID: PMC3812400.
      Citations: 67     Fields:    Translation:AnimalsCells
    22. Friesner RA, Shivakumar D, Harder E, Damm W, 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.
      Citations: 104     Fields:    
    23. 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; PMCID: PMC2838399.
      Citations: 112     Fields:    
    24. 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.
      Citations: 11     Fields:    Translation:Cells
    25. 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; PMCID: PMC2880651.
      Citations: 31     Fields:    
    26. 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; PMCID: PMC2671189.
      Citations: 23     Fields:    
    27. 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; PMCID: PMC4754998.
      Citations: 45     Fields:    Translation:Cells
    28. 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; PMCID: PMC3141218.
      Citations: 17     Fields:    
    29. 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.
      Citations: 48     Fields:    
    30. 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; PMCID: PMC2742603.
      Citations: 11     Fields:    
    31. 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; PMCID: PMC1187998.
      Citations: 11     Fields:    
    32. 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.
      Citations: 12     Fields:    Translation:Cells
    33. 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.
      Citations: 17     Fields:    
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