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    Ken Dill, PhD

    SchoolUCSF School of Pharmacy
    DepartmentPharmaceutical Chemistry
    Address600 16th Street
    San Francisco CA 94158
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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. 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.
        View in: PubMed
      2. 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.
        View in: PubMed
      3. 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.
        View in: PubMed
      4. 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.
        View in: PubMed
      5. 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.
        View in: PubMed
      6. 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.
        View in: PubMed
      7. 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.
        View in: PubMed
      8. 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.
        View in: PubMed
      9. Rollins GC, Dill KA. General mechanism of two-state protein folding kinetics. J Am Chem Soc. 2014 Aug 13; 136(32):11420-7.
        View in: PubMed
      10. 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.
        View in: PubMed
      11. 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.
        View in: PubMed PMC4064692
      12. 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.
        View in: PubMed PMC4142335
      13. 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.
        View in: PubMed
      14. 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.
        View in: PubMed PMC4065164
      15. 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.
        View in: PubMed PMC3905753
      16. 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.
        View in: PubMed PMC3870711
      17. 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.
        View in: PubMed PMC3838431
      18. 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.
        View in: PubMed
      19. 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.
        View in: PubMed PMC3962782
      20. 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.
        View in: PubMed PMC3598757
      21. 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.
        View in: PubMed PMC3893241
      22. 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.
        View in: PubMed PMC3569860
      23. Dill KA. Biophysics. Introduction. Annu Rev Biophys. 2013; 42.
        View in: PubMed
      24. Dill KA, MacCallum JL. The protein-folding problem, 50 years on. Science. 2012 Nov 23; 338(6110):1042-6.
        View in: PubMed
      25. Urbic T, Fennell CJ, Dill KA. A microscopic theory of solvation of monoions. Acta Chim Slov. 2012 Sep; 59(3):554-8.
        View in: PubMed
      26. 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.
        View in: PubMed PMC3437879
      27. Peterson GJ, Pressé S, Peterson KS, Dill KA. Simulated evolution of protein-protein interaction networks with realistic topology. PLoS One. 2012; 7(6):e39052.
        View in: PubMed PMC3387198
      28. 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.
        View in: PubMed
      29. Fennell CJ, Li L, Dill KA. Simple liquid models with corrected dielectric constants. J Phys Chem B. 2012 Jun 14; 116(23):6936-44.
        View in: PubMed PMC3729351
      30. Schmit JD, Dill K. Growth rates of protein crystals. J Am Chem Soc. 2012 Mar 7; 134(9):3934-7.
        View in: PubMed PMC3311159
      31. 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.
        View in: PubMed PMC3292588
      32. 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.
        View in: PubMed
      33. 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.
        View in: PubMed PMC3207669
      34. 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.
        View in: PubMed PMC3238793
      35. 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.
        View in: PubMed PMC3182083
      36. 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.
        View in: PubMed PMC3098004
      37. 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.
        View in: PubMed PMC3044389
      38. 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.
        View in: PubMed PMC3021675
      39. Voelz VA, Dill KA, Chorny I. Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER. Biopolymers. 2011; 96(5):639-50.
        View in: PubMed
      40. Ghosh K, Dill K. Cellular proteomes have broad distributions of protein stability. Biophys J. 2010 Dec 15; 99(12):3996-4002.
        View in: PubMed PMC3000515
      41. 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.
        View in: PubMed PMC3004097
      42. 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.
        View in: PubMed
      43. 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.
        View in: PubMed PMC2941273
      44. Urbic T, Dill KA. A statistical mechanical theory for a two-dimensional model of water. J Chem Phys. 2010 Jun 14; 132(22):224507.
        View in: PubMed PMC2902533
      45. 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.
        View in: PubMed PMC4142491
      46. Schmit JD, Dill KA. The stabilities of protein crystals. J Phys Chem B. 2010 Mar 25; 114(11):4020-7.
        View in: PubMed PMC2919244
      47. 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.
        View in: PubMed PMC2810857
      48. 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.
        View in: PubMed PMC2792327
      49. 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.
        View in: PubMed
      50. 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.
        View in: PubMed PMC2788029
      51. 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.
        View in: PubMed PMC3273425
      52. 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.
        View in: PubMed PMC2705543
      53. 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.
        View in: PubMed PMC2698044
      54. 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.
        View in: PubMed PMC2756098
      55. 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.
        View in: PubMed PMC2684682
      56. 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.
        View in: PubMed PMC2832024
      57. Ghosh K, Dill KA. Theory for protein folding cooperativity: helix bundles. J Am Chem Soc. 2009 Feb 18; 131(6):2306-12.
        View in: PubMed PMC2654554
      58. 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.
        View in: PubMed PMC2629132
      59. 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.
        View in: PubMed PMC2716649
      60. 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.
        View in: PubMed PMC2801025
      61. 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.
        View in: PubMed PMC2639212
      62. Wu GA, Coutsias EA, Dill KA. Iterative assembly of helical proteins by optimal hydrophobic packing. Structure. 2008 Aug 6; 16(8):1257-66.
        View in: PubMed PMC2629734
      63. 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.
        View in: PubMed PMC2748234
      64. 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.
        View in: PubMed PMC2671656
      65. 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.
        View in: PubMed PMC2699260
      66. 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.
        View in: PubMed PMC2745216
      67. 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.
        View in: PubMed PMC2745223
      68. Dill KA, Ozkan SB, Shell MS, Weikl TR. The protein folding problem. Annu Rev Biophys. 2008; 37:289-316.
        View in: PubMed PMC2443096
      69. 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.
        View in: PubMed
      70. 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.
        View in: PubMed
      71. 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.
        View in: PubMed
      72. 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.
        View in: PubMed PMC1924571
      73. 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.
        View in: PubMed
      74. 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.
        View in: PubMed PMC2104542
      75. 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.
        View in: PubMed PMC1891208
      76. 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.
        View in: PubMed
      77. 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.
        View in: PubMed
      78. Voelz VA, Dill KA. Exploring zipping and assembly as a protein folding principle. Proteins. 2007 Mar 1; 66(4):877-88.
        View in: PubMed
      79. 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.
        View in: PubMed PMC3261839
      80. 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.
        View in: PubMed
      81. Hockenmaier J, Joshi AK, Dill KA. Routes are trees: the parsing perspective on protein folding. Proteins. 2007 Jan 1; 66(1):1-15.
        View in: PubMed
      82. 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.
        View in: PubMed
      83. 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.
        View in: PubMed PMC3583553
      84. Ho BK, Dill KA. Folding very short peptides using molecular dynamics. PLoS Comput Biol. 2006 Apr; 2(4):e27.
        View in: PubMed PMC1435986
      85. Urbic T, Vlachy V, Dill KA. Confined water: a Mercedes-Benz model study. J Phys Chem B. 2006 Mar 16; 110(10):4963-70.
        View in: PubMed
      86. 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.
        View in: PubMed
      87. Chorny I, Dill KA, Jacobson MP. Surfaces affect ion pairing. J Phys Chem B. 2005 Dec 22; 109(50):24056-60.
        View in: PubMed
      88. 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.
        View in: PubMed
      89. 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.
        View in: PubMed
      90. 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.
        View in: PubMed
      91. 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.
        View in: PubMed PMC1177393
      92. 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.
        View in: PubMed PMC2253451
      93. 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.
        View in: PubMed
      94. 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.
        View in: PubMed
      95. Coutsias EA, Seok C, Dill KA. Using quaternions to calculate RMSD. J Comput Chem. 2004 Nov 30; 25(15):1849-57.
        View in: PubMed
      96. Weikl TR, Palassini M, Dill KA. Cooperativity in two-state protein folding kinetics. Protein Sci. 2004 Mar; 13(3):822-9.
        View in: PubMed PMC2286727
      97. Coutsias EA, Seok C, Jacobson MP, Dill KA. A kinematic view of loop closure. J Comput Chem. 2004 Mar; 25(4):510-28.
        View in: PubMed
      98. 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.
        View in: PubMed
      99. 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.
        View in: PubMed
      100. Schonbrun J, Dill KA. Fast protein folding kinetics. Proc Natl Acad Sci U S A. 2003 Oct 28; 100(22):12678-82.
        View in: PubMed PMC240677
      101. 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.
        View in: PubMed
      102. Truskett TM, Dill KA. A simple analytical model of water. Biophys Chem. 2003 Sep; 105(2-3):449-59.
        View in: PubMed
      103. 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.
        View in: PubMed
      104. 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.
        View in: PubMed
      105. 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.
        View in: PubMed
      106. Ozkan SB, Dill KA, Bahar I. Computing the transition state populations in simple protein models. Biopolymers. 2003 Jan; 68(1):35-46.
        View in: PubMed
      107. 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.
        View in: PubMed
      108. Southall NT, Dill KA. Potential of mean force between two hydrophobic solutes in water. Biophys Chem. 2002 Dec 10; 101-102:295-307.
        View in: PubMed
      109. 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.
        View in: PubMed PMC1513647
      110. 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.
        View in: PubMed PMC2373683
      111. Ball KD, Erman B, Dill KA. The elastic net algorithm and protein structure prediction. J Comput Chem. 2002 Jan 15; 23(1):77-83.
        View in: PubMed
      112. Zhou HX, Dill KA. Stabilization of proteins in confined spaces. Biochemistry. 2001 Sep 25; 40(38):11289-93.
        View in: PubMed
      113. 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.
        View in: PubMed
      114. Liang J, Dill KA. Are proteins well-packed? Biophys J. 2001 Aug; 81(2):751-66.
        View in: PubMed PMC1301551
      115. 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.
        View in: PubMed
      116. Rosen JB, Phillips AT, Oh SY, Dill KA. A method for parameter optimization in computational biology. Biophys J. 2000 Dec; 79(6):2818-24.
        View in: PubMed PMC1301162
      117. Yue K, Dill KA. Constraint-based assembly of tertiary protein structures from secondary structure elements. Protein Sci. 2000 Oct; 9(10):1935-46.
        View in: PubMed PMC2144474
      118. Chen SJ, Dill KA. RNA folding energy landscapes. Proc Natl Acad Sci U S A. 2000 Jan 18; 97(2):646-51.
        View in: PubMed PMC15384
      119. Young M, Kirshenbaum K, Dill KA, Highsmith S. Predicting conformational switches in proteins. Protein Sci. 1999 Sep; 8(9):1752-64.
        View in: PubMed PMC2144394
      120. Kirshenbaum K, Zuckermann RN, Dill KA. Designing polymers that mimic biomolecules. Curr Opin Struct Biol. 1999 Aug; 9(4):530-5.
        View in: PubMed
      121. Dill KA. Strengthening biomedicine's roots. Nature. 1999 Jul 22; 400(6742):309-10.
        View in: PubMed
      122. Dill KA. Polymer principles and protein folding. Protein Sci. 1999 Jun; 8(6):1166-80.
        View in: PubMed PMC2144345
      123. 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.
        View in: PubMed PMC2144332
      124. Ishikawa K, Yue K, Dill KA. Predicting the structures of 18 peptides using Geocore. Protein Sci. 1999 Apr; 8(4):716-21.
        View in: PubMed PMC2144307
      125. 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.
        View in: PubMed
      126. 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.
        View in: PubMed PMC22485
      127. 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.
        View in: PubMed PMC22484
      128. Chan HS, Dill KA. Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics. Proteins. 1998 Jan; 30(1):2-33.
        View in: PubMed
      129. Miller DW, Dill KA. Ligand binding to proteins: the binding landscape model. Protein Sci. 1997 Oct; 6(10):2166-79.
        View in: PubMed PMC2143563
      130. Dill KA. Additivity principles in biochemistry. J Biol Chem. 1997 Jan 10; 272(2):701-4.
        View in: PubMed
      131. Chan HS, Dill KA. Solvation: how to obtain microscopic energies from partitioning and solvation experiments. Annu Rev Biophys Biomol Struct. 1997; 26:425-59.
        View in: PubMed
      132. Dill KA, Chan HS. From Levinthal to pathways to funnels. Nat Struct Biol. 1997 Jan; 4(1):10-9.
        View in: PubMed
      133. 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.
        View in: PubMed
      134. 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.
        View in: PubMed
      135. 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.
        View in: PubMed PMC38109
      136. Stigter D, Dill KA. Binding of ionic ligands to polyelectrolytes. Biophys J. 1996 Oct; 71(4):2064-74.
        View in: PubMed PMC1233673
      137. 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.
        View in: PubMed PMC2143263
      138. Thomas PD, Dill KA. Statistical potentials extracted from protein structures: how accurate are they? J Mol Biol. 1996 Mar 29; 257(2):457-69.
        View in: PubMed
      139. Chan HS, Dill KA. A simple model of chaperonin-mediated protein folding. Proteins. 1996 Mar; 24(3):345-51.
        View in: PubMed
      140. Chan HS, Dill KA. Comparing folding codes for proteins and polymers. Proteins. 1996 Mar; 24(3):335-44.
        View in: PubMed
      141. Yue K, Dill KA. Folding proteins with a simple energy function and extensive conformational searching. Protein Sci. 1996 Feb; 5(2):254-61.
        View in: PubMed PMC2143350
      142. 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.
        View in: PubMed
      143. Miller DW, Dill KA. A statistical mechanical model for hydrogen exchange in globular proteins. Protein Sci. 1995 Sep; 4(9):1860-73.
        View in: PubMed PMC2143224
      144. 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.
        View in: PubMed
      145. 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.
        View in: PubMed
      146. 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.
        View in: PubMed PMC2143098
      147. 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.
        View in: PubMed PMC42871
      148. 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.
        View in: PubMed PMC42834
      149. Dill KA, Stigter D. Modeling protein stability as heteropolymer collapse. Adv Protein Chem. 1995; 46:59-104.
        View in: PubMed
      150. 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.
        View in: PubMed
      151. Bromberg S, Dill KA. Side-chain entropy and packing in proteins. Protein Sci. 1994 Jul; 3(7):997-1009.
        View in: PubMed PMC2142898
      152. Lattman EE, Fiebig KM, Dill KA. Modeling compact denatured states of proteins. Biochemistry. 1994 May 24; 33(20):6158-66.
        View in: PubMed
      153. Bennett DW, Dill K. Theoretical study of arsenical-antidote adducts. Drug Chem Toxicol. 1994; 17(1):69-73.
        View in: PubMed
      154. Thomas PD, Dill KA. Local and nonlocal interactions in globular proteins and mechanisms of alcohol denaturation. Protein Sci. 1993 Dec; 2(12):2050-65.
        View in: PubMed PMC2142326
      155. Yee DP, Dill KA. Families and the structural relatedness among globular proteins. Protein Sci. 1993 Jun; 2(6):884-99.
        View in: PubMed PMC2142412
      156. De Young LR, Dill KA, Fink AL. Aggregation and denaturation of apomyoglobin in aqueous urea solutions. Biochemistry. 1993 Apr 20; 32(15):3877-86.
        View in: PubMed
      157. 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.
        View in: PubMed PMC45996
      158. 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.
        View in: PubMed
      159. Stickle DF, Presta LG, Dill KA, Rose GD. Hydrogen bonding in globular proteins. J Mol Biol. 1992 Aug 20; 226(4):1143-59.
        View in: PubMed
      160. Stigter D, Mingins J, Dill KA. Phospholipid interactions in model membrane systems. II. Theory. Biophys J. 1992 Jun; 61(6):1616-29.
        View in: PubMed PMC1260455
      161. Mingins J, Stigter D, Dill KA. Phospholipid interactions in model membrane systems. I. Experiments on monolayers. Biophys J. 1992 Jun; 61(6):1603-15.
        View in: PubMed PMC1260454
      162. 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.
        View in: PubMed PMC525653
      163. 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.
        View in: PubMed PMC2142194
      164. 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.
        View in: PubMed
      165. Alonso DO, Dill KA, Stigter D. The three states of globular proteins: acid denaturation. Biopolymers. 1991 Nov; 31(13):1631-49.
        View in: PubMed
      166. Alonso DO, Dill KA. Solvent denaturation and stabilization of globular proteins. Biochemistry. 1991 Jun 18; 30(24):5974-85.
        View in: PubMed
      167. 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.
        View in: PubMed
      168. 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.
        View in: PubMed
      169. 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.
        View in: PubMed PMC51621
      170. 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.
        View in: PubMed
      171. Chan HS, Dill KA. Polymer principles in protein structure and stability. Annu Rev Biophys Biophys Chem. 1991; 20:447-90.
        View in: PubMed
      172. Dill KA, Shortle D. Denatured states of proteins. Annu Rev Biochem. 1991; 60:795-825.
        View in: PubMed
      173. Dill KA. The meaning of hydrophobicity. Science. 1990 Oct 12; 250(4978):297-8.
        View in: PubMed
      174. 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.
        View in: PubMed
      175. Dill KA. Dominant forces in protein folding. Biochemistry. 1990 Aug 7; 29(31):7133-55.
        View in: PubMed
      176. Chan HS, Dill KA. Origins of structure in globular proteins. Proc Natl Acad Sci U S A. 1990 Aug; 87(16):6388-92.
        View in: PubMed PMC54539
      177. Stigter D, Dill KA. Charge effects on folded and unfolded proteins. Biochemistry. 1990 Feb 6; 29(5):1262-71.
        View in: PubMed
      178. Lau KF, Dill KA. Theory for protein mutability and biogenesis. Proc Natl Acad Sci U S A. 1990 Jan; 87(2):638-42.
        View in: PubMed PMC53320
      179. 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.
        View in: PubMed
      180. Dill KA, Alonso DO, Hutchinson K. Thermal stabilities of globular proteins. Biochemistry. 1989 Jun 27; 28(13):5439-49.
        View in: PubMed
      181. Chong S, Dill K, McGown E. The interaction of phenyldichloroarsine with erythrocytes. J Biochem Toxicol. 1989; 4(1):39-45.
        View in: PubMed
      182. De Young LR, Dill KA. Solute partitioning into lipid bilayer membranes. Biochemistry. 1988 Jul 12; 27(14):5281-9.
        View in: PubMed
      183. 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.
        View in: PubMed
      184. Dill KA, Naghizadeh J, Marqusee JA. Chain molecules at high densities at interfaces. Annu Rev Phys Chem. 1988; 39:425-61.
        View in: PubMed
      185. Dill KA. Protein surgery. Protein Eng. 1987 Oct-Nov; 1(5):369-71.
        View in: PubMed
      186. Dill KA. The chain conformations in membranes and micelles. Adv Colloid Interface Sci. 1986 Nov; 26(2-4):99-110.
        View in: PubMed
      187. 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.
        View in: PubMed
      188. Dill KA. Theory for the folding and stability of globular proteins. Biochemistry. 1985 Mar 12; 24(6):1501-9.
        View in: PubMed
      189. 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.
        View in: PubMed
      190. 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.
        View in: PubMed
      191. Dill KA. Theory for the separation of very large DNA molecules by radial migration. Biophys Chem. 1979 Nov; 10(3-4):327-34.
        View in: PubMed
      192. Dill KA, Zimm BH. A rhelogical separator for very large DNA molecules. Nucleic Acids Res. 1979 Oct 10; 7(3):735-49.
        View in: PubMed PMC328052
      193. 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.
        View in: PubMed
      194. 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.
        View in: PubMed
      195. 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.
        View in: PubMed
      196. 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.
        View in: PubMed
      197. 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.
        View in: PubMed
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