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    Ken Dill, PhD

    TitleProfessor
    SchoolUCSF School of Pharmacy
    DepartmentPharmaceutical Chemistry
    Address600 16th Street
    San Francisco CA 94158
    Phone415-476-9964
    vCardDownload vCard

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      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Wagoner JA, Dill KA. Molecular Motors: Power Strokes Outperform Brownian Ratchets. J Phys Chem B. 2016 Jul 7; 120(26):6327-36. PMID: 27136319.
        View in: PubMed
      2. Maitra A, Dill KA. Modeling the Overproduction of Ribosomes when Antibacterial Drugs Act on Cells. Biophys J. 2016 Feb 2; 110(3):743-8. PMID: 26840738.
        View in: PubMed
      3. Perez A, Morrone JA, Simmerling C, Dill KA. Advances in free-energy-based simulations of protein folding and ligand binding. Curr Opin Struct Biol. 2016 Feb; 36:25-31. PMID: 26773233.
        View in: PubMed
      4. Perez A, MacCallum JL, Coutsias EA, Dill KA. Constraint methods that accelerate free-energy simulations of biomolecules. J Chem Phys. 2015 Dec 28; 143(24):243143. PMID: 26723628.
        View in: PubMed
      5. Holm C, Gompper G, Dill KA. Preface: Special Topic on Coarse Graining of Macromolecules, Biopolymers, and Membranes. J Chem Phys. 2015 Dec 28; 143(24):242901. PMID: 26723585.
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      6. de Graff AM, Hazoglou MJ, Dill KA. Highly Charged Proteins: The Achilles' Heel of Aging Proteomes. Structure. 2016 Feb 2; 24(2):329-36. PMID: 26724998.
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      7. Dixit PD, Jain A, Stock G, Dill KA. Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes. J Chem Theory Comput. 2015 Nov 10; 11(11):5464-72. PMID: 26574334.
        View in: PubMed
      8. Perez A, MacCallum JL, Brini E, Simmerling C, Dill KA. Grid-Based Backbone Correction to the ff12SB Protein Force Field for Implicit-Solvent Simulations. J Chem Theory Comput. 2015 Oct 13; 11(10):4770-9. PMID: 26574266.
        View in: PubMed
      9. Perez A, MacCallum JL, Dill KA. Accelerating molecular simulations of proteins using Bayesian inference on weak information. Proc Natl Acad Sci U S A. 2015 Sep 22; 112(38):11846-51. PMID: 26351667; PMCID: PMC4586851.
      10. Hazoglou MJ, Walther V, Dixit PD, Dill KA. Communication: Maximum caliber is a general variational principle for nonequilibrium statistical mechanics. J Chem Phys. 2015 Aug 7; 143(5):051104. PMID: 26254635.
        View in: PubMed
      11. MacCallum JL, Perez A, Dill KA. Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference. Proc Natl Acad Sci U S A. 2015 Jun 2; 112(22):6985-90. PMID: 26038552; PMCID: PMC4460504.
      12. Kastelic M, Kalyuzhnyi YV, Hribar-Lee B, Dill KA, Vlachy V. Protein aggregation in salt solutions. Proc Natl Acad Sci U S A. 2015 May 26; 112(21):6766-70. PMID: 25964322; PMCID: PMC4450416 [Available on 11/26/15].
      13. Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations. J Chem Theory Comput. 2015 Mar 10; 11(3):1347. PMID: 26579779.
        View in: PubMed
      14. Maitra A, Dill KA. Bacterial growth laws reflect the evolutionary importance of energy efficiency. Proc Natl Acad Sci U S A. 2015 Jan 13; 112(2):406-11. PMID: 25548180; PMCID: PMC4299221.
      15. Sharma VK, Patapoff TW, Kabakoff B, Pai S, Hilario E, Zhang B, Li C, Borisov O, Kelley RF, Chorny I, Zhou JZ, Dill KA, Swartz TE. In silico selection of therapeutic antibodies for development: viscosity, clearance, and chemical stability. Proc Natl Acad Sci U S A. 2014 Dec 30; 111(52):18601-6. PMID: 25512516; PMCID: PMC4284567.
      16. Li L, Fennell CJ, Dill KA. Small molecule solvation changes due to the presence of salt are governed by the cost of solvent cavity formation and dispersion. J Chem Phys. 2014 Dec 14; 141(22):22D518. PMID: 25494789; PMCID: PMC4241710 [Available on 12/14/15].
      17. Cohen P, Dill KA, Jaswal SS. Modeling the solvation of nonpolar amino acids in guanidinium chloride solutions. J Phys Chem B. 2014 Sep 11; 118(36):10618-23. PMID: 25141127.
        View in: PubMed
      18. Rollins GC, Dill KA. General mechanism of two-state protein folding kinetics. J Am Chem Soc. 2014 Aug 13; 136(32):11420-7. PMID: 25056406.
        View in: PubMed
      19. Perez A, Roy A, Kasavajhala K, Wagaman A, Dill KA, MacCallum JL. Extracting representative structures from protein conformational ensembles. Proteins. 2014 Oct; 82(10):2671-80. PMID: 24975328.
        View in: PubMed
      20. Pressé S, Peterson J, Lee J, Elms P, MacCallum JL, Marqusee S, Bustamante C, Dill K. Single molecule conformational memory extraction: p5ab RNA hairpin. J Phys Chem B. 2014 Jun 19; 118(24):6597-603. PMID: 24898871; PMCID: PMC4064692.
      21. Lukšic M, Fennell CJ, Dill KA. Using interpolation for fast and accurate calculation of ion-ion interactions. J Phys Chem B. 2014 Jul 17; 118(28):8017-25. PMID: 24625086; PMCID: PMC4142335.
      22. Li L, Dill KA, Fennell CJ. Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge. J Comput Aided Mol Des. 2014 Mar; 28(3):259-64. PMID: 24474161.
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      23. Li L, Fennell CJ, Dill KA. Field-SEA: a model for computing the solvation free energies of nonpolar, polar, and charged solutes in water. J Phys Chem B. 2014 Jun 19; 118(24):6431-7. PMID: 24299013; PMCID: PMC4065164.
      24. Roy A, Perez A, Dill KA, Maccallum JL. Computing the relative stabilities and the per-residue components in protein conformational changes. Structure. 2014 Jan 7; 22(1):168-75. PMID: 24316402; PMCID: PMC3905753.
      25. Peterson J, Dixit PD, Dill KA. A maximum entropy framework for nonexponential distributions. Proc Natl Acad Sci U S A. 2013 Dec 17; 110(51):20380-5. PMID: 24297895; PMCID: PMC3870711.
      26. Rocklin GJ, Mobley DL, Dill KA, Hünenberger PH. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects. J Chem Phys. 2013 Nov 14; 139(18):184103. PMID: 24320250; PMCID: PMC3838431.
      27. Pressé S, Ghosh K, Lee J, Dill KA. Nonadditive entropies yield probability distributions with biases not warranted by the data. Phys Rev Lett. 2013 Nov 1; 111(18):180604. PMID: 24237501.
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      28. Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA. Blind prediction of charged ligand binding affinities in a model binding site. J Mol Biol. 2013 Nov 15; 425(22):4569-83. PMID: 23896298; PMCID: PMC3962782.
      29. Rocklin GJ, Mobley DL, Dill KA. Separated topologies--a method for relative binding free energy calculations using orientational restraints. J Chem Phys. 2013 Feb 28; 138(8):085104. PMID: 23464180; PMCID: PMC3598757.
      30. Kortkhonjia E, Brandman R, Zhou JZ, Voelz VA, Chorny I, Kabakoff B, Patapoff TW, Dill KA, Swartz TE. Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations. MAbs. 2013 Mar-Apr; 5(2):306-22. PMID: 23396076; PMCID: PMC3893241.
      31. Pressé S, Lee J, Dill KA. Extracting conformational memory from single-molecule kinetic data. J Phys Chem B. 2013 Jan 17; 117(2):495-502. PMID: 23259771; PMCID: PMC3569860.
      32. Dill KA. Biophysics. Introduction. Annu Rev Biophys. 2013; 42. PMID: 23798065.
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      33. Dill KA, MacCallum JL. The protein-folding problem, 50 years on. Science. 2012 Nov 23; 338(6110):1042-6. PMID: 23180855.
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      34. Urbic T, Fennell CJ, Dill KA. A microscopic theory of solvation of monoions. Acta Chim Slov. 2012 Sep; 59(3):554-8. PMID: 24061310.
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      35. Butterfoss GL, Yoo B, Jaworski JN, Chorny I, Dill KA, Zuckermann RN, Bonneau R, Kirshenbaum K, Voelz VA. De novo structure prediction and experimental characterization of folded peptoid oligomers. Proc Natl Acad Sci U S A. 2012 Sep 4; 109(36):14320-5. PMID: 22908242; PMCID: PMC3437879.
      36. Peterson GJ, Pressé S, Peterson KS, Dill KA. Simulated evolution of protein-protein interaction networks with realistic topology. PLoS One. 2012; 7(6):e39052. PMID: 22768057; PMCID: PMC3387198.
      37. Lukšic M, Urbic T, Hribar-Lee B, Dill KA. Simple model of hydrophobic hydration. J Phys Chem B. 2012 May 31; 116(21):6177-86. PMID: 22564051.
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      38. Fennell CJ, Li L, Dill KA. Simple liquid models with corrected dielectric constants. J Phys Chem B. 2012 Jun 14; 116(23):6936-44. PMID: 22397577; PMCID: PMC3729351.
      39. Schmit JD, Dill K. Growth rates of protein crystals. J Am Chem Soc. 2012 Mar 7; 134(9):3934-7. PMID: 22339624; PMCID: PMC3311159.
      40. Ge H, Pressé S, Ghosh K, Dill KA. Markov processes follow from the principle of maximum caliber. J Chem Phys. 2012 Feb 14; 136(6):064108. PMID: 22360170; PMCID: PMC3292588.
      41. Kehoe CW, Fennell CJ, Dill KA. Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test. J Comput Aided Mol Des. 2012 May; 26(5):563-8. PMID: 22205387.
        View in: PubMed
      42. Dill KA, Ghosh K, Schmit JD. Physical limits of cells and proteomes. Proc Natl Acad Sci U S A. 2011 Nov 1; 108(44):17876-82. PMID: 22006304; PMCID: PMC3207669.
      43. MacCallum JL, Pérez A, Schnieders MJ, Hua L, Jacobson MP, Dill KA. Assessment of protein structure refinement in CASP9. Proteins. 2011; 79 Suppl 10:74-90. PMID: 22069034; PMCID: PMC3238793.
      44. Schmit JD, Whitelam S, Dill K. Electrostatics and aggregation: how charge can turn a crystal into a gel. J Chem Phys. 2011 Aug 28; 135(8):085103. PMID: 21895221; PMCID: PMC3182083.
      45. Pressé S, Ghosh K, Dill KA. Modeling stochastic dynamics in biochemical systems with feedback using maximum caliber. J Phys Chem B. 2011 May 19; 115(19):6202-12. PMID: 21524067; PMCID: PMC3098004.
      46. Fennell CJ, Kehoe CW, Dill KA. Modeling aqueous solvation with semi-explicit assembly. Proc Natl Acad Sci U S A. 2011 Feb 22; 108(8):3234-9. PMID: 21300905; PMCID: PMC3044389.
      47. Schmit JD, Ghosh K, Dill K. What drives amyloid molecules to assemble into oligomers and fibrils? Biophys J. 2011 Jan 19; 100(2):450-8. PMID: 21244841; PMCID: PMC3021675.
      48. Voelz VA, Dill KA, Chorny I. Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER. Biopolymers. 2011; 96(5):639-50. PMID: 21184487.
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      49. Ghosh K, Dill K. Cellular proteomes have broad distributions of protein stability. Biophys J. 2010 Dec 15; 99(12):3996-4002. PMID: 21156142; PMCID: PMC3000515.
      50. Hribar-Lee B, Dill KA, Vlachy V. Receptacle model of salting-in by tetramethylammonium ions. J Phys Chem B. 2010 Nov 25; 114(46):15085-91. PMID: 21028768; PMCID: PMC3004097.
      51. Pressé S, Ghosh K, Phillips R, Dill KA. Dynamical fluctuations in biochemical reactions and cycles. Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Sep; 82(3 Pt 1):031905. PMID: 21230106.
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      52. Peterson GJ, Pressé S, Dill KA. Nonuniversal power law scaling in the probability distribution of scientific citations. Proc Natl Acad Sci U S A. 2010 Sep 14; 107(37):16023-7. PMID: 20805513; PMCID: PMC2941273.
      53. Urbic T, Dill KA. A statistical mechanical theory for a two-dimensional model of water. J Chem Phys. 2010 Jun 14; 132(22):224507. PMID: 20550408; PMCID: PMC2902533.
      54. Kalyuzhnyi YV, Vlachy V, Dill KA. Aqueous alkali halide solutions: can osmotic coefficients be explained on the basis of the ionic sizes alone? Phys Chem Chem Phys. 2010 Jun 21; 12(23):6260-6. PMID: 20405084; PMCID: PMC4142491.
      55. Schmit JD, Dill KA. The stabilities of protein crystals. J Phys Chem B. 2010 Mar 25; 114(11):4020-7. PMID: 20199035; PMCID: PMC2919244.
      56. Fennell CJ, Kehoe C, Dill KA. Oil/water transfer is partly driven by molecular shape, not just size. J Am Chem Soc. 2010 Jan 13; 132(1):234-40. PMID: 19961159; PMCID: PMC2810857.
      57. Bizjak A, Urbic T, Vlachy V, Dill KA. Theory for the three-dimensional Mercedes-Benz model of water. J Chem Phys. 2009 Nov 21; 131(19):194504. PMID: 19929057; PMCID: PMC2792327.
      58. Druchok M, Vlachy V, Dill KA. Computer simulations of ionenes, hydrophobic ions with unusual solution thermodynamic properties. The ion-specific effects. J Phys Chem B. 2009 Oct 29; 113(43):14270-6. PMID: 19799433.
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      59. Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill KA, Shoichet BK. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J Mol Biol. 2009 Dec 11; 394(4):747-63. PMID: 19782087; PMCID: PMC2788029.
      60. Wu D, Ghosh K, Inamdar M, Lee HJ, Fraser S, Dill K, Phillips R. Trajectory approach to two-state kinetics of single particles on sculpted energy landscapes. Phys Rev Lett. 2009 Jul 31; 103(5):050603. PMID: 19792475; PMCID: PMC3273425.
      61. Ghosh K, Dill KA. Computing protein stabilities from their chain lengths. Proc Natl Acad Sci U S A. 2009 Jun 30; 106(26):10649-54. PMID: 19541647; PMCID: PMC2705543.
      62. Fennell CJ, Bizjak A, Vlachy V, Dill KA. Ion pairing in molecular simulations of aqueous alkali halide solutions. J Phys Chem B. 2009 May 14; 113(19):6782-91. PMID: 19206510; PMCID: PMC2698044.
      63. Mobley DL, Dill KA. Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Structure. 2009 Apr 15; 17(4):489-98. PMID: 19368882; PMCID: PMC2756098.
      64. Mobley DL, Bayly CI, Cooper MD, Dill KA. Predictions of hydration free energies from all-atom molecular dynamics simulations. J Phys Chem B. 2009 Apr 9; 113(14):4533-7. PMID: 19271713; PMCID: PMC2684682.
      65. Druchok M, Vlachy V, Dill KA. Explicit-water molecular dynamics study of a short-chain 3,3 ionene in solutions with sodium halides. J Chem Phys. 2009 Apr 7; 130(13):134903. PMID: 19355776; PMCID: PMC2832024.
      66. Ghosh K, Dill KA. Theory for protein folding cooperativity: helix bundles. J Am Chem Soc. 2009 Feb 18; 131(6):2306-12. PMID: 19170581; PMCID: PMC2654554.
      67. Voelz VA, Shell MS, Dill KA. Predicting peptide structures in native proteins from physical simulations of fragments. PLoS Comput Biol. 2009 Feb; 5(2):e1000281. PMID: 19197352; PMCID: PMC2629132.
      68. Shell MS, Ozkan SB, Voelz V, Wu GA, Dill KA. Blind test of physics-based prediction of protein structures. Biophys J. 2009 Feb; 96(3):917-24. PMID: 19186130; PMCID: PMC2716649.
      69. MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson MP, Dill KA. Assessment of the protein-structure refinement category in CASP8. Proteins. 2009; 77 Suppl 9:66-80. PMID: 19714776; PMCID: PMC2801025.
      70. Watkins GA, Jones EF, Scott Shell M, VanBrocklin HF, Pan MH, Hanrahan SM, Feng JJ, He J, Sounni NE, Dill KA, Contag CH, Coussens LM, Franc BL. Development of an optimized activatable MMP-14 targeted SPECT imaging probe. Bioorg Med Chem. 2009 Jan 15; 17(2):653-9. PMID: 19109023; PMCID: PMC2639212.
      71. Wu GA, Coutsias EA, Dill KA. Iterative assembly of helical proteins by optimal hydrophobic packing. Structure. 2008 Aug 6; 16(8):1257-66. PMID: 18682227; PMCID: PMC2629734.
      72. Lee BC, Chu TK, Dill KA, Zuckermann RN. Biomimetic nanostructures: creating a high-affinity zinc-binding site in a folded nonbiological polymer. J Am Chem Soc. 2008 Jul 9; 130(27):8847-55. PMID: 18597438; PMCID: PMC2748234.
      73. Stock G, Ghosh K, Dill KA. Maximum Caliber: a variational approach applied to two-state dynamics. J Chem Phys. 2008 May 21; 128(19):194102. PMID: 18500851; PMCID: PMC2671656.
      74. Shell MS, Ritterson R, Dill KA. A test on peptide stability of AMBER force fields with implicit solvation. J Phys Chem B. 2008 Jun 5; 112(22):6878-86. PMID: 18471007; PMCID: PMC2699260.
      75. Mobley DL, Baker JR, Barber AE, Fennell CJ, Dill KA. Charge asymmetries in hydration of polar solutes. J Phys Chem B. 2008 Feb 28; 112(8):2405-14. PMID: 18251538; PMCID: PMC2745216.
      76. Mobley DL, Dill KA, Chodera JD. Treating entropy and conformational changes in implicit solvent simulations of small molecules. J Phys Chem B. 2008 Jan 24; 112(3):938-46. PMID: 18171044; PMCID: PMC2745223.
      77. Dill KA, Ozkan SB, Shell MS, Weikl TR. The protein folding problem. Annu Rev Biophys. 2008; 37:289-316. PMID: 18573083; PMCID: PMC2443096.
      78. Urbic T, Vlachy V, Kalyuzhnyi YV, Dill KA. An improved thermodynamic perturbation theory for Mercedes-Benz water. J Chem Phys. 2007 Nov 7; 127(17):174511. PMID: 17994831.
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      79. Urbic T, Vlachy V, Kalyuzhnyi YV, Dill KA. Theory for the solvation of nonpolar solutes in water. J Chem Phys. 2007 Nov 7; 127(17):174505. PMID: 17994825.
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      80. Ghosh K, Ozkan SB, Dill KA. The ultimate speed limit to protein folding is conformational searching. J Am Chem Soc. 2007 Oct 3; 129(39):11920-7. PMID: 17824609.
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      81. Ozkan SB, Wu GA, Chodera JD, Dill KA. Protein folding by zipping and assembly. Proc Natl Acad Sci U S A. 2007 Jul 17; 104(29):11987-92. PMID: 17620603; PMCID: PMC1924571.
      82. Dill KA, Ozkan SB, Weikl TR, Chodera JD, Voelz VA. The protein folding problem: when will it be solved? Curr Opin Struct Biol. 2007 Jun; 17(3):342-6. PMID: 17572080.
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      83. Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA. Predicting absolute ligand binding free energies to a simple model site. J Mol Biol. 2007 Aug 24; 371(4):1118-34. PMID: 17599350; PMCID: PMC2104542.
      84. Bradford JA, Dill KA. Stochastic innovation as a mechanism by which catalysts might self-assemble into chemical reaction networks. Proc Natl Acad Sci U S A. 2007 Jun 12; 104(24):10098-103. PMID: 17548812; PMCID: PMC1891208.
      85. Chodera JD, Singhal N, Pande VS, Dill KA, Swope WC. Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. J Chem Phys. 2007 Apr 21; 126(15):155101. PMID: 17461665.
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      86. Lucas A, Huang L, Joshi A, Dill KA. Statistical mechanics of helix bundles using a dynamic programming approach. J Am Chem Soc. 2007 Apr 11; 129(14):4272-81. PMID: 17362002.
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      87. Voelz VA, Dill KA. Exploring zipping and assembly as a protein folding principle. Proteins. 2007 Mar 1; 66(4):877-88. PMID: 17154424.
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      88. Seitaridou E, Inamdar MM, Phillips R, Ghosh K, Dill K. Measuring flux distributions for diffusion in the small-numbers limit. J Phys Chem B. 2007 Mar 8; 111(9):2288-92. PMID: 17295536; PMCID: PMC3261839.
      89. Mobley DL, Dumont E, Chodera JD, Dill KA. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. J Phys Chem B. 2007 Mar 8; 111(9):2242-54. PMID: 17291029.
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      90. Hockenmaier J, Joshi AK, Dill KA. Routes are trees: the parsing perspective on protein folding. Proteins. 2007 Jan 1; 66(1):1-15. PMID: 17063473.
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      91. Chodera JD, Swope WC, Pitera JW, Seok C, Dill KA. Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations. J Chem Theory Comput. 2007 Jan; 3(1):26-41. PMID: 26627148.
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      92. Weikl TR, Dill KA. Transition-states in protein folding kinetics: the structural interpretation of Phi values. J Mol Biol. 2007 Feb 2; 365(5):1578-86. PMID: 17141267.
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      93. Mobley DL, Chodera JD, Dill KA. On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. J Chem Phys. 2006 Aug 28; 125(8):084902. PMID: 16965052; PMCID: PMC3583553.
      94. Ho BK, Dill KA. Folding very short peptides using molecular dynamics. PLoS Comput Biol. 2006 Apr; 2(4):e27. PMID: 16617376; PMCID: PMC1435986.
      95. Urbic T, Vlachy V, Dill KA. Confined water: a Mercedes-Benz model study. J Phys Chem B. 2006 Mar 16; 110(10):4963-70. PMID: 16526737.
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      96. Chiang D, Joshi AK, Dill KA. A grammatical theory for the conformational changes of simple helix bundles. J Comput Biol. 2006 Jan-Feb; 13(1):21-42. PMID: 16472020.
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      97. Chorny I, Dill KA, Jacobson MP. Surfaces affect ion pairing. J Phys Chem B. 2005 Dec 22; 109(50):24056-60. PMID: 16375397.
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      98. Xu H, Dill KA. Water's hydrogen bonds in the hydrophobic effect: a simple model. J Phys Chem B. 2005 Dec 15; 109(49):23611-7. PMID: 16375338.
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      99. Coutsias EA, Seok C, Dill KA. Rotational superposition and least squares: the SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller. J Comput Chem. 2005 Nov 30; 26(15):1663-5. PMID: 16175579.
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      100. Lee BC, Zuckermann RN, Dill KA. Folding a nonbiological polymer into a compact multihelical structure. J Am Chem Soc. 2005 Aug 10; 127(31):10999-1009. PMID: 16076207.
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      101. Merlo C, Dill KA, Weikl TR. Phi values in protein-folding kinetics have energetic and structural components. Proc Natl Acad Sci U S A. 2005 Jul 19; 102(29):10171-5. PMID: 16009941; PMCID: PMC1177393.
      102. Ho BK, Coutsias EA, Seok C, Dill KA. The flexibility in the proline ring couples to the protein backbone. Protein Sci. 2005 Apr; 14(4):1011-8. PMID: 15772308; PMCID: PMC2253451.
      103. Jaswal SS, Truhlar SM, Dill KA, Agard DA. Comprehensive analysis of protein folding activation thermodynamics reveals a universal behavior violated by kinetically stable proteases. J Mol Biol. 2005 Mar 25; 347(2):355-66. PMID: 15740746.
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      104. Dill KA, Truskett TM, Vlachy V, Hribar-Lee B. Modeling water, the hydrophobic effect, and ion solvation. Annu Rev Biophys Biomol Struct. 2005; 34:173-99. PMID: 15869376.
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      105. Coutsias EA, Seok C, Dill KA. Using quaternions to calculate RMSD. J Comput Chem. 2004 Nov 30; 25(15):1849-57. PMID: 15376254.
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      106. Weikl TR, Palassini M, Dill KA. Cooperativity in two-state protein folding kinetics. Protein Sci. 2004 Mar; 13(3):822-9. PMID: 14978313; PMCID: PMC2286727.
      107. Coutsias EA, Seok C, Jacobson MP, Dill KA. A kinematic view of loop closure. J Comput Chem. 2004 Mar; 25(4):510-28. PMID: 14735570.
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      108. Horn T, Lee BC, Dill KA, Zuckermann RN. Incorporation of chemoselective functionalities into peptoids via solid-phase submonomer synthesis. Bioconjug Chem. 2004 Mar-Apr; 15(2):428-35. PMID: 15025542.
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      109. Wu CW, Kirshenbaum K, Sanborn TJ, Patch JA, Huang K, Dill KA, Zuckermann RN, Barron AE. Structural and spectroscopic studies of peptoid oligomers with alpha-chiral aliphatic side chains. J Am Chem Soc. 2003 Nov 5; 125(44):13525-30. PMID: 14583049.
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      110. Schonbrun J, Dill KA. Fast protein folding kinetics. Proc Natl Acad Sci U S A. 2003 Oct 28; 100(22):12678-82. PMID: 14569019; PMCID: PMC240677.
      111. Weikl TR, Dill KA. Folding kinetics of two-state proteins: effect of circularization, permutation, and crosslinks. J Mol Biol. 2003 Sep 26; 332(4):953-63. PMID: 12972264.
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      112. Truskett TM, Dill KA. A simple analytical model of water. Biophys Chem. 2003 Sep; 105(2-3):449-59. PMID: 14499910.
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      113. Weikl TR, Dill KA. Folding rates and low-entropy-loss routes of two-state proteins. J Mol Biol. 2003 Jun 6; 329(3):585-98. PMID: 12767836.
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      114. Seok C, Rosen JB, Chodera JD, Dill KA. MOPED: method for optimizing physical energy parameters using decoys. J Comput Chem. 2003 Jan 15; 24(1):89-97. PMID: 12483678.
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      115. Amato NM, Dill KA, Song G. Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures. J Comput Biol. 2003; 10(3-4):239-55. PMID: 12935327.
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      116. Ozkan SB, Dill KA, Bahar I. Computing the transition state populations in simple protein models. Biopolymers. 2003 Jan; 68(1):35-46. PMID: 12579578.
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      117. Song G, Thomas S, Dill KA, Scholtz JM, Amato NM. A path planning-based study of protein folding with a case study of hairpin formation in protein G and L. Pac Symp Biocomput. 2003; 240-51. PMID: 12603032.
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      118. Southall NT, Dill KA. Potential of mean force between two hydrophobic solutes in water. Biophys Chem. 2002 Dec 10; 101-102:295-307. PMID: 12488009.
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      119. Hribar B, Southall NT, Vlachy V, Dill KA. How ions affect the structure of water. J Am Chem Soc. 2002 Oct 16; 124(41):12302-11. PMID: 12371874; PMCID: PMC1513647.
      120. Ozkan SB, Dill KA, Bahar I. Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model. Protein Sci. 2002 Aug; 11(8):1958-70. PMID: 12142450; PMCID: PMC2373683.
      121. Ball KD, Erman B, Dill KA. The elastic net algorithm and protein structure prediction. J Comput Chem. 2002 Jan 15; 23(1):77-83. PMID: 11913391.
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      122. Zhou HX, Dill KA. Stabilization of proteins in confined spaces. Biochemistry. 2001 Sep 25; 40(38):11289-93. PMID: 11560476.
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      123. Ozkan SB, Bahar I, Dill KA. Transition states and the meaning of Phi-values in protein folding kinetics. Nat Struct Biol. 2001 Sep; 8(9):765-9. PMID: 11524678.
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      124. Liang J, Dill KA. Are proteins well-packed? Biophys J. 2001 Aug; 81(2):751-66. PMID: 11463623; PMCID: PMC1301551.
      125. Mitchell KJ, Pinson KI, Kelly OG, Brennan J, Zupicich J, Scherz P, Leighton PA, Goodrich LV, Lu X, Avery BJ, Tate P, Dill K, Pangilinan E, Wakenight P, Tessier-Lavigne M, Skarnes WC. Functional analysis of secreted and transmembrane proteins critical to mouse development. Nat Genet. 2001 Jul; 28(3):241-9. PMID: 11431694.
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      126. Rosen JB, Phillips AT, Oh SY, Dill KA. A method for parameter optimization in computational biology. Biophys J. 2000 Dec; 79(6):2818-24. PMID: 11106591; PMCID: PMC1301162.
      127. Yue K, Dill KA. Constraint-based assembly of tertiary protein structures from secondary structure elements. Protein Sci. 2000 Oct; 9(10):1935-46. PMID: 11106167; PMCID: PMC2144474.
      128. Chen SJ, Dill KA. RNA folding energy landscapes. Proc Natl Acad Sci U S A. 2000 Jan 18; 97(2):646-51. PMID: 10639133; PMCID: PMC15384.
      129. Young M, Kirshenbaum K, Dill KA, Highsmith S. Predicting conformational switches in proteins. Protein Sci. 1999 Sep; 8(9):1752-64. PMID: 10493576; PMCID: PMC2144394.
      130. Kirshenbaum K, Zuckermann RN, Dill KA. Designing polymers that mimic biomolecules. Curr Opin Struct Biol. 1999 Aug; 9(4):530-5. PMID: 10449369.
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      131. Dill KA. Strengthening biomedicine's roots. Nature. 1999 Jul 22; 400(6742):309-10. PMID: 10432104.
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      132. Dill KA. Polymer principles and protein folding. Protein Sci. 1999 Jun; 8(6):1166-80. PMID: 10386867; PMCID: PMC2144345.
      133. Brem R, Dill KA. The effect of multiple binding modes on empirical modeling of ligand docking to proteins. Protein Sci. 1999 May; 8(5):1134-43. PMID: 10338024; PMCID: PMC2144332.
      134. Ishikawa K, Yue K, Dill KA. Predicting the structures of 18 peptides using Geocore. Protein Sci. 1999 Apr; 8(4):716-21. PMID: 10211817; PMCID: PMC2144307.
      135. Tang KE, Dill KA. Native protein fluctuations: the conformational-motion temperature and the inverse correlation of protein flexibility with protein stability. J Biomol Struct Dyn. 1998 Oct; 16(2):397-411. PMID: 9833677.
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      136. Armand P, Kirshenbaum K, Goldsmith RA, Farr-Jones S, Barron AE, Truong KT, Dill KA, Mierke DF, Cohen FE, Zuckermann RN, Bradley EK. NMR determination of the major solution conformation of a peptoid pentamer with chiral side chains. Proc Natl Acad Sci U S A. 1998 Apr 14; 95(8):4309-14. PMID: 9539733; PMCID: PMC22485.
      137. Kirshenbaum K, Barron AE, Goldsmith RA, Armand P, Bradley EK, Truong KT, Dill KA, Cohen FE, Zuckermann RN. Sequence-specific polypeptoids: a diverse family of heteropolymers with stable secondary structure. Proc Natl Acad Sci U S A. 1998 Apr 14; 95(8):4303-8. PMID: 9539732; PMCID: PMC22484.
      138. Chan HS, Dill KA. Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics. Proteins. 1998 Jan; 30(1):2-33. PMID: 9443337.
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      139. Miller DW, Dill KA. Ligand binding to proteins: the binding landscape model. Protein Sci. 1997 Oct; 6(10):2166-79. PMID: 9336839; PMCID: PMC2143563.
      140. Dill KA. Additivity principles in biochemistry. J Biol Chem. 1997 Jan 10; 272(2):701-4. PMID: 8995351.
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      141. Chan HS, Dill KA. Solvation: how to obtain microscopic energies from partitioning and solvation experiments. Annu Rev Biophys Biomol Struct. 1997; 26:425-59. PMID: 9241426.
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      142. Dill KA, Chan HS. From Levinthal to pathways to funnels. Nat Struct Biol. 1997 Jan; 4(1):10-9. PMID: 8989315.
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      143. Armand P, Kirshenbaum K, Falicov A, Dunbrack RL, Dill KA, Zuckermann RN, Cohen FE. Chiral N-substituted glycines can form stable helical conformations. Fold Des. 1997; 2(6):369-75. PMID: 9427011.
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      144. Dill KA, Phillips AT, Rosen JB. Protein structure and energy landscape dependence on sequence using a continuous energy function. J Comput Biol. 1997; 4(3):227-39. PMID: 9278057.
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      145. Chan SD, Dill K, Blomdahl J, Wada HG. Nonisotopic quantitation of mRNA using a novel RNase protection assay: measurement of erbB-2 mRNA in tumor cell lines. Anal Biochem. 1996 Nov 15; 242(2):214-20. PMID: 8937564.
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      146. Thomas PD, Dill KA. An iterative method for extracting energy-like quantities from protein structures. Proc Natl Acad Sci U S A. 1996 Oct 15; 93(21):11628-33. PMID: 8876187; PMCID: PMC38109.
      147. Stigter D, Dill KA. Binding of ionic ligands to polyelectrolytes. Biophys J. 1996 Oct; 71(4):2064-74. PMID: 8889181; PMCID: PMC1233673.
      148. Beutler TC, Dill KA. A fast conformational search strategy for finding low energy structures of model proteins. Protein Sci. 1996 Oct; 5(10):2037-43. PMID: 8897604; PMCID: PMC2143263.
      149. Thomas PD, Dill KA. Statistical potentials extracted from protein structures: how accurate are they? J Mol Biol. 1996 Mar 29; 257(2):457-69. PMID: 8609636.
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      150. Chan HS, Dill KA. A simple model of chaperonin-mediated protein folding. Proteins. 1996 Mar; 24(3):345-51. PMID: 8778781.
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      151. Chan HS, Dill KA. Comparing folding codes for proteins and polymers. Proteins. 1996 Mar; 24(3):335-44. PMID: 8778780.
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      152. Yue K, Dill KA. Folding proteins with a simple energy function and extensive conformational searching. Protein Sci. 1996 Feb; 5(2):254-61. PMID: 8745403; PMCID: PMC2143350.
      153. Sun S, Brem R, Chan HS, Dill KA. Designing amino acid sequences to fold with good hydrophobic cores. Protein Eng. 1995 Dec; 8(12):1205-13. PMID: 8869633.
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      154. Miller DW, Dill KA. A statistical mechanical model for hydrogen exchange in globular proteins. Protein Sci. 1995 Sep; 4(9):1860-73. PMID: 8528084; PMCID: PMC2143224.
      155. Sun S, Thomas PD, Dill KA. A simple protein folding algorithm using a binary code and secondary structure constraints. Protein Eng. 1995 Aug; 8(8):769-78. PMID: 8637846.
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      156. Chan HS, Bromberg S, Dill KA. Models of cooperativity in protein folding. Philos Trans R Soc Lond B Biol Sci. 1995 Apr 29; 348(1323):61-70. PMID: 7770488.
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      157. Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, Thomas PD, Chan HS. Principles of protein folding--a perspective from simple exact models. Protein Sci. 1995 Apr; 4(4):561-602. PMID: 7613459; PMCID: PMC2143098.
      158. Yue K, Fiebig KM, Thomas PD, Chan HS, Shakhnovich EI, Dill KA. A test of lattice protein folding algorithms. Proc Natl Acad Sci U S A. 1995 Jan 3; 92(1):325-9. PMID: 7816842; PMCID: PMC42871.
      159. Yue K, Dill KA. Forces of tertiary structural organization in globular proteins. Proc Natl Acad Sci U S A. 1995 Jan 3; 92(1):146-50. PMID: 7816806; PMCID: PMC42834.
      160. Dill KA, Stigter D. Modeling protein stability as heteropolymer collapse. Adv Protein Chem. 1995; 46:59-104. PMID: 7771323.
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      161. Yee DP, Chan HS, Havel TF, Dill KA. Does compactness induce secondary structure in proteins? A study of poly-alanine chains computed by distance geometry. J Mol Biol. 1994 Aug 26; 241(4):557-73. PMID: 8057379.
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      162. Bromberg S, Dill KA. Side-chain entropy and packing in proteins. Protein Sci. 1994 Jul; 3(7):997-1009. PMID: 7920265; PMCID: PMC2142898.
      163. Lattman EE, Fiebig KM, Dill KA. Modeling compact denatured states of proteins. Biochemistry. 1994 May 24; 33(20):6158-66. PMID: 8193129.
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      164. Bennett DW, Dill K. Theoretical study of arsenical-antidote adducts. Drug Chem Toxicol. 1994; 17(1):69-73. PMID: 8168434.
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      165. Thomas PD, Dill KA. Local and nonlocal interactions in globular proteins and mechanisms of alcohol denaturation. Protein Sci. 1993 Dec; 2(12):2050-65. PMID: 8298455; PMCID: PMC2142326.
      166. Yee DP, Dill KA. Families and the structural relatedness among globular proteins. Protein Sci. 1993 Jun; 2(6):884-99. PMID: 8318894; PMCID: PMC2142412.
      167. De Young LR, Dill KA, Fink AL. Aggregation and denaturation of apomyoglobin in aqueous urea solutions. Biochemistry. 1993 Apr 20; 32(15):3877-86. PMID: 8471600.
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      168. Dill KA, Fiebig KM, Chan HS. Cooperativity in protein-folding kinetics. Proc Natl Acad Sci U S A. 1993 Mar 1; 90(5):1942-6. PMID: 7680482; PMCID: PMC45996.
      169. McGown EL, Dill K, O'Connor RJ, Khan M, LeTellier YC, Vandegriff KD. Regeneration of functional hemoglobin from iron(III) hemoglobin by reduction with hydrogen and a heterogeneous catalyst. Anal Biochem. 1992 Nov 15; 207(1):85-9. PMID: 1489103.
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      170. Stickle DF, Presta LG, Dill KA, Rose GD. Hydrogen bonding in globular proteins. J Mol Biol. 1992 Aug 20; 226(4):1143-59. PMID: 1518048.
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      171. Stigter D, Mingins J, Dill KA. Phospholipid interactions in model membrane systems. II. Theory. Biophys J. 1992 Jun; 61(6):1616-29. PMID: 1617141; PMCID: PMC1260455.
      172. Mingins J, Stigter D, Dill KA. Phospholipid interactions in model membrane systems. I. Experiments on monolayers. Biophys J. 1992 Jun; 61(6):1603-15. PMID: 1617140; PMCID: PMC1260454.
      173. Yue K, Dill KA. Inverse protein folding problem: designing polymer sequences. Proc Natl Acad Sci U S A. 1992 May 1; 89(9):4163-7. PMID: 1570343; PMCID: PMC525653.
      174. Shortle D, Chan HS, Dill KA. Modeling the effects of mutations on the denatured states of proteins. Protein Sci. 1992 Feb; 1(2):201-15. PMID: 1304903; PMCID: PMC2142194.
      175. Bennett DW, Huang LH, Dill K. Semiempirical self-consistent field (CNDO) calculations of arsenical-antidote adducts. Chem Res Toxicol. 1992 Jan-Feb; 5(1):5-7. PMID: 1581536.
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      176. Alonso DO, Dill KA, Stigter D. The three states of globular proteins: acid denaturation. Biopolymers. 1991 Nov; 31(13):1631-49. PMID: 1814509.
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      177. Alonso DO, Dill KA. Solvent denaturation and stabilization of globular proteins. Biochemistry. 1991 Jun 18; 30(24):5974-85. PMID: 2043635.
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      178. Kollman PA, Dill KA. Decisions in force field development: an alternative to those described by Roterman et al. (J. Biomol. Struct. Dyn. 7, 421 (1989)). J Biomol Struct Dyn. 1991 Jun; 8(6):1103-7; discussion 1109-11. PMID: 1892580.
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      179. Dill K, Huang LH, McGown EL, Youn SH, O'Connor RJ. Substituent effects on the binding constants of arsenical-dithiol adducts. Res Commun Chem Pathol Pharmacol. 1991 Jun; 72(3):367-70. PMID: 1947439.
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      180. Stigter D, Alonso DO, Dill KA. Protein stability: electrostatics and compact denatured states. Proc Natl Acad Sci U S A. 1991 May 15; 88(10):4176-80. PMID: 2034662; PMCID: PMC51621.
      181. Dill K, Huang LH, Bearden DW, McGown EL, O'Connor RJ. Activation energies and formation rate constants for organic arsenical-antidote adducts as determined by dynamic NMR spectroscopy. Chem Res Toxicol. 1991 May-Jun; 4(3):295-9. PMID: 1912312.
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      182. Chan HS, Dill KA. Polymer principles in protein structure and stability. Annu Rev Biophys Biophys Chem. 1991; 20:447-90. PMID: 1867723.
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      183. Dill KA, Shortle D. Denatured states of proteins. Annu Rev Biochem. 1991; 60:795-825. PMID: 1883209.
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      184. Dill KA. The meaning of hydrophobicity. Science. 1990 Oct 12; 250(4978):297-8. PMID: 2218535.
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      185. O'Connor RJ, McGown EL, Dill K, Hallowell SF. Relative binding constants of arsenical-antidote adducts determined by NMR spectroscopy. Res Commun Chem Pathol Pharmacol. 1990 Sep; 69(3):365-8. PMID: 2173085.
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      186. Dill KA. Dominant forces in protein folding. Biochemistry. 1990 Aug 7; 29(31):7133-55. PMID: 2207096.
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      187. Chan HS, Dill KA. Origins of structure in globular proteins. Proc Natl Acad Sci U S A. 1990 Aug; 87(16):6388-92. PMID: 2385597; PMCID: PMC54539.
      188. Stigter D, Dill KA. Charge effects on folded and unfolded proteins. Biochemistry. 1990 Feb 6; 29(5):1262-71. PMID: 2322561.
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      189. Lau KF, Dill KA. Theory for protein mutability and biogenesis. Proc Natl Acad Sci U S A. 1990 Jan; 87(2):638-42. PMID: 2300551; PMCID: PMC53320.
      190. Ying PT, Dorsey JG, Dill KA. Retention mechanisms of reversed-phase liquid chromatography: determination of solute-solvent interaction free energies. Anal Chem. 1989 Nov 15; 61(22):2540-6. PMID: 2817406.
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      191. Dill KA, Alonso DO, Hutchinson K. Thermal stabilities of globular proteins. Biochemistry. 1989 Jun 27; 28(13):5439-49. PMID: 2775715.
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      192. Chong S, Dill K, McGown E. The interaction of phenyldichloroarsine with erythrocytes. J Biochem Toxicol. 1989; 4(1):39-45. PMID: 2769696.
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      193. De Young LR, Dill KA. Solute partitioning into lipid bilayer membranes. Biochemistry. 1988 Jul 12; 27(14):5281-9. PMID: 3167046.
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      194. Dill KA, Stigter D. Lateral interactions among phosphatidylcholine and phosphatidylethanolamine head groups in phospholipid monolayers and bilayers. Biochemistry. 1988 May 3; 27(9):3446-53. PMID: 3390444.
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      195. Dill KA, Naghizadeh J, Marqusee JA. Chain molecules at high densities at interfaces. Annu Rev Phys Chem. 1988; 39:425-61. PMID: 3075466.
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      196. Dill KA. Protein surgery. Protein Eng. 1987 Oct-Nov; 1(5):369-71. PMID: 3508283.
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      197. Dill KA. The chain conformations in membranes and micelles. Adv Colloid Interface Sci. 1986 Nov; 26(2-4):99-110. PMID: 3333135.
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      198. Lannom HK, Dill K, Denarié M, LaCombe JM, Pavia AA. 13C n.m.r. study of the structure and the metal ion binding sites of neuropeptides composed of L-Asp and L-Glu. Int J Pept Protein Res. 1986 Jul; 28(1):67-78. PMID: 2875970.
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      199. Dill KA. Theory for the folding and stability of globular proteins. Biochemistry. 1985 Mar 12; 24(6):1501-9. PMID: 3986190.
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      200. Tullis RH, Dill KA, Price PA. Fluorescence and kinetic studies on the divalent metal ion induced conformational changes in DNase a. J Biol Chem. 1981 Jun 10; 256(11):5656-61. PMID: 7240163.
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      201. Dill KA, Flory PJ. Interphases of chain molecules: Monolayers and lipid bilayer membranes. Proc Natl Acad Sci U S A. 1980 Jun; 77(6):3115-9. PMID: 16592834.
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      202. Dill KA. Theory for the separation of very large DNA molecules by radial migration. Biophys Chem. 1979 Nov; 10(3-4):327-34. PMID: 16997227.
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      203. Dill KA, Zimm BH. A rhelogical separator for very large DNA molecules. Nucleic Acids Res. 1979 Oct 10; 7(3):735-49. PMID: 388346; PMCID: PMC328052.
      204. Dill K, Satterlee JD, Richards JH. 13C Nuclear magnetic resonance studies to the binding of isocyanides to various hemoglobins and myoglobins. Biochemistry. 1978 Oct 3; 17(20):4291-8. PMID: 708715.
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      205. Dill K, Allerhand A. Effect of chemical modifications at tryptophan-108 on binding of lanthanide ions to hen egg-white lysozyme. Application of natural-abundance carbon-13 nuclear magnetic resonance spectroscopy. Biochemistry. 1977 Dec 27; 16(26):5711-6. PMID: 563241.
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      206. Dill K, Allerhand A. Studies of individual methine aromatic carbon sites of proteins by natural-abundance carbon-13 nuclear magnetic resonance spectroscopy at high magnetic field strengths. J Am Chem Soc. 1977 Jun 22; 99(13):4508-11. PMID: 864126.
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      207. Moon RB, Dill K, Richards JH. Magnetic resonance studies of the binding of 13C-labeled carbon monoxide to myoglobins and hemoglobins containing modified hemes. Biochemistry. 1977 Jan 25; 16(2):221-8. PMID: 13807.
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      208. Dill K, Shafer RH. Radial migration of DNA molecules in cylindrical flow. III. Circles and the effect of non-gaussian polymer statistics. Biophys Chem. 1976 Jan; 4(1):51-4. PMID: 1247650.
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