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Ken Dill, PhD

TitleProfessor Emeritus
InstitutionUniversity of California San Francisco
DepartmentPharmaceutical Chemistry
Address600 16th St
San Francisco CA 94158
Phone415-476-9964
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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, Sittel F, Stock G, Dill K. MELD-Path Efficiently Computes Conformational Transitions, Including Multiple and Diverse Paths. J Chem Theory Comput. 2018 Apr 10; 14(4):2109-2116. PMID: 29547695.
      View in: PubMed
    2. Dixit PD, Dill K. Caliber Corrected Markov Modeling (C2M2): Correcting Equilibrium Markov Models. J Chem Theory Comput. 2018 Feb 13; 14(2):1111-1119. PMID: 29323898.
      View in: PubMed
    3. Dixit PD, Wagoner J, Weistuch C, Pressé S, Ghosh K, Dill K. Perspective: Maximum caliber is a general variational principle for dynamical systems. J Chem Phys. 2018 Jan 07; 148(1):010901. PMID: 29306272.
      View in: PubMed
    4. Brini E, Fennell CJ, Fernandez-Serra M, Hribar-Lee B, Lukšic M, Dill K. How Water's Properties Are Encoded in Its Molecular Structure and Energies. Chem Rev. 2017 Oct 11; 117(19):12385-12414. PMID: 28949513.
      View in: PubMed
    5. Urbic T, Dill K. Analytical theory of the hydrophobic effect of solutes in water. Phys Rev E. 2017 Sep; 96(3-1):032101. PMID: 29347026.
      View in: PubMed
    6. Guseva E, Zuckermann RN, Dill K. Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers. Proc Natl Acad Sci U S A. 2017 Sep 05; 114(36):E7460-E7468. PMID: 28831002.
      View in: PubMed
    7. Szenk M, Dill K, de Graff AMR. Why Do Fast-Growing Bacteria Enter Overflow Metabolism? Testing the Membrane Real Estate Hypothesis. Cell Syst. 2017 Aug 23; 5(2):95-104. PMID: 28755958.
      View in: PubMed
    8. Perez A, Morrone JA, Dill K. Accelerating physical simulations of proteins by leveraging external knowledge. Wiley Interdiscip Rev Comput Mol Sci. 2017 Sep-Oct; 7(5). PMID: 28959358.
      View in: PubMed
    9. Santra M, Farrell DW, Dill K. Bacterial proteostasis balances energy and chaperone utilization efficiently. Proc Natl Acad Sci U S A. 2017 03 28; 114(13):E2654-E2661. PMID: 28292901.
      View in: PubMed
    10. Morrone JA, Perez A, Deng Q, Ha SN, Holloway MK, Sawyer TK, Sherborne BS, Brown FK, Dill K. Molecular Simulations Identify Binding Poses and Approximate Affinities of Stapled a-Helical Peptides to MDM2 and MDMX. J Chem Theory Comput. 2017 Feb 14; 13(2):863-869. PMID: 28042965.
      View in: PubMed
    11. Morrone JA, Perez A, MacCallum J, Dill K. Computed Binding of Peptides to Proteins with MELD-Accelerated Molecular Dynamics. J Chem Theory Comput. 2017 Feb 14; 13(2):870-876. PMID: 28042966.
      View in: PubMed
    12. Perez A, Morrone JA, Brini E, MacCallum JL, Dill K. Blind protein structure prediction using accelerated free-energy simulations. Sci Adv. 2016 Nov; 2(11):e1601274. PMID: 27847872.
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    13. Brini E, Paranahewage SS, Fennell CJ, Dill K. Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules. J Comput Aided Mol Des. 2016 Nov; 30(11):1067-1077. PMID: 27632227.
      View in: PubMed
    14. Ghosh K, de Graff AM, Sawle L, Dill K. Role of Proteome Physical Chemistry in Cell Behavior. J Phys Chem B. 2016 09 15; 120(36):9549-63. PMID: 27513457.
      View in: PubMed
    15. Wagoner JA, Dill K. Molecular Motors: Power Strokes Outperform Brownian Ratchets. J Phys Chem B. 2016 07 07; 120(26):6327-36. PMID: 27136319.
      View in: PubMed
    16. Maitra A, Dill K. Modeling the Overproduction of Ribosomes when Antibacterial Drugs Act on Cells. Biophys J. 2016 Feb 02; 110(3):743-748. PMID: 26840738; PMCID: PMC4744161 [Available on 02/02/17].
    17. Perez A, Morrone JA, Simmerling C, Dill K. Advances in free-energy-based simulations of protein folding and ligand binding. Curr Opin Struct Biol. 2016 Feb; 36:25-31. PMID: 26773233; PMCID: PMC4785060 [Available on 02/01/17].
    18. Perez A, MacCallum JL, Coutsias EA, Dill K. Constraint methods that accelerate free-energy simulations of biomolecules. J Chem Phys. 2015 Dec 28; 143(24):243143. PMID: 26723628; PMCID: PMC4684272 [Available on 12/28/16].
    19. Holm C, Gompper G, Dill K. 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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    20. de Graff AM, Hazoglou MJ, Dill K. Highly Charged Proteins: The Achilles' Heel of Aging Proteomes. Structure. 2016 Feb 02; 24(2):329-36. PMID: 26724998.
      View in: PubMed
    21. Dixit PD, Jain A, Stock G, Dill K. 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
    22. Perez A, MacCallum JL, Brini E, Simmerling C, Dill K. 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; PMCID: PMC4813323 [Available on 10/13/16].
    23. Perez A, MacCallum JL, Dill K. 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.
    24. Hazoglou MJ, Walther V, Dixit PD, Dill K. Communication: Maximum caliber is a general variational principle for nonequilibrium statistical mechanics. J Chem Phys. 2015 Aug 07; 143(5):051104. PMID: 26254635.
      View in: PubMed
    25. MacCallum JL, Perez A, Dill K. Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference. Proc Natl Acad Sci U S A. 2015 Jun 02; 112(22):6985-90. PMID: 26038552; PMCID: PMC4460504.
    26. Kastelic M, Kalyuzhnyi YV, Hribar-Lee B, Dill K, 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.
    27. Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill K. 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; PMCID: PMC4675652.
    28. Maitra A, Dill K. 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.
    29. Sharma VK, Patapoff TW, Kabakoff B, Pai S, Hilario E, Zhang B, Li C, Borisov O, Kelley RF, Chorny I, Zhou JZ, Dill K, 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.
    30. Li L, Fennell CJ, Dill K. 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.
    31. Cohen P, Dill K, 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.
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    32. Rollins GC, Dill K. General mechanism of two-state protein folding kinetics. J Am Chem Soc. 2014 Aug 13; 136(32):11420-7. PMID: 25056406.
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    33. Drechsel NJ, Fennell CJ, Dill K, Villà-Freixa J. TRIFORCE: Tessellated Semianalytical Solvent Exposed Surface Areas and Derivatives. J Chem Theory Comput. 2014 Sep 09; 10(9):4121-4132. PMID: 25221446.
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    34. Perez A, Roy A, Kasavajhala K, Wagaman A, Dill K, MacCallum JL. Extracting representative structures from protein conformational ensembles. Proteins. 2014 Oct; 82(10):2671-80. PMID: 24975328.
      View in: PubMed
    35. 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.
    36. Dixit PD, Dill K. Inferring Microscopic Kinetic Rates from Stationary State Distributions. J Chem Theory Comput. 2014 Aug 12; 10(8):3002-3005. PMID: 25136269.
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    37. Lukšic M, Fennell CJ, Dill K. 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.
    38. Li L, Dill K, 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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    39. Li L, Fennell CJ, Dill K. 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.
    40. Roy A, Perez A, Dill K, Maccallum JL. Computing the relative stabilities and the per-residue components in protein conformational changes. Structure. 2014 Jan 07; 22(1):168-75. PMID: 24316402; PMCID: PMC3905753.
    41. Peterson J, Dixit PD, Dill K. 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.
    42. Rocklin GJ, Mobley DL, Dill K, 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.
    43. Pressé S, Ghosh K, Lee J, Dill K. Nonadditive entropies yield probability distributions with biases not warranted by the data. Phys Rev Lett. 2013 Nov 01; 111(18):180604. PMID: 24237501.
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    44. Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill K. 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.
    45. Rocklin GJ, Mobley DL, Dill K. Calculating the sensitivity and robustness of binding free energy calculations to force field parameters. J Chem Theory Comput. 2013 Jul 09; 9(7):3072-3083. PMID: 24015114.
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    46. Rocklin GJ, Mobley DL, Dill K. 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.
    47. Kortkhonjia E, Brandman R, Zhou JZ, Voelz VA, Chorny I, Kabakoff B, Patapoff TW, Dill K, 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.
    48. Pressé S, Lee J, Dill K. Extracting conformational memory from single-molecule kinetic data. J Phys Chem B. 2013 Jan 17; 117(2):495-502. PMID: 23259771; PMCID: PMC3569860.
    49. Dill K. Biophysics. Introduction. Annu Rev Biophys. 2013; 42. PMID: 23798065.
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    50. Dill K, MacCallum JL. The protein-folding problem, 50 years on. Science. 2012 Nov 23; 338(6110):1042-6. PMID: 23180855.
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    51. Perez A, Yang Z, Bahar I, Dill K, MacCallum JL. FlexE: Using elastic network models to compare models of protein structure. J Chem Theory Comput. 2012 Oct 09; 8(10):3985-3991. PMID: 25530735.
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    52. Urbic T, Fennell CJ, Dill K. A microscopic theory of solvation of monoions. Acta Chim Slov. 2012 Sep; 59(3):554-8. PMID: 24061310.
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    53. Butterfoss GL, Yoo B, Jaworski JN, Chorny I, Dill K, 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 04; 109(36):14320-5. PMID: 22908242; PMCID: PMC3437879.
    54. Peterson GJ, Pressé S, Peterson KS, Dill K. Simulated evolution of protein-protein interaction networks with realistic topology. PLoS One. 2012; 7(6):e39052. PMID: 22768057.
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    55. Lukšic M, Urbic T, Hribar-Lee B, Dill K. Simple model of hydrophobic hydration. J Phys Chem B. 2012 May 31; 116(21):6177-86. PMID: 22564051.
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    56. Fennell CJ, Li L, Dill K. Simple liquid models with corrected dielectric constants. J Phys Chem B. 2012 Jun 14; 116(23):6936-44. PMID: 22397577; PMCID: PMC3729351.
    57. Schmit JD, Dill K. Growth rates of protein crystals. J Am Chem Soc. 2012 Mar 07; 134(9):3934-7. PMID: 22339624; PMCID: PMC3311159.
    58. Ge H, Pressé S, Ghosh K, Dill K. Markov processes follow from the principle of maximum caliber. J Chem Phys. 2012 Feb 14; 136(6):064108. PMID: 22360170; PMCID: PMC3292588.
    59. Kehoe CW, Fennell CJ, Dill K. 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.
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    60. Dill K, Ghosh K, Schmit JD. Physical limits of cells and proteomes. Proc Natl Acad Sci U S A. 2011 Nov 01; 108(44):17876-82. PMID: 22006304; PMCID: PMC3207669.
    61. Fennell CJ, Dill K. Physical Modeling of Aqueous Solvation. J Stat Phys. 2011 Oct 01; 145(2):209-226. PMID: 25143658.
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    62. MacCallum JL, Pérez A, Schnieders MJ, Hua L, Jacobson MP, Dill K. Assessment of protein structure refinement in CASP9. Proteins. 2011; 79 Suppl 10:74-90. PMID: 22069034; PMCID: PMC3238793.
    63. 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.
    64. Fennell CJ, Kehoe CW, Dill K. 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.
    65. 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.
    66. Voelz VA, Dill K, 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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    67. 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.
    68. Hribar-Lee B, Dill K, 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.
    69. Peterson GJ, Pressé S, Dill K. 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.
    70. Urbic T, Dill K. A statistical mechanical theory for a two-dimensional model of water. J Chem Phys. 2010 Jun 14; 132(22):224507. PMID: 20550408; PMCID: PMC2902533.
    71. Kalyuzhnyi YV, Vlachy V, Dill K. 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.
    72. Schmit JD, Dill K. The stabilities of protein crystals. J Phys Chem B. 2010 Mar 25; 114(11):4020-7. PMID: 20199035; PMCID: PMC2919244.
    73. Fennell CJ, Kehoe C, Dill K. 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.
    74. Bizjak A, Urbic T, Vlachy V, Dill K. Theory for the three-dimensional Mercedes-Benz model of water. J Chem Phys. 2009 Nov 21; 131(19):194504. PMID: 19929057; PMCID: PMC2792327.
    75. Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill K, 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.
    76. 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.
    77. Ghosh K, Dill K. 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.
    78. Fennell CJ, Bizjak A, Vlachy V, Dill K. Ion pairing in molecular simulations of aqueous alkali halide solutions. J Phys Chem B. 2009 May 14; 113(19):6782-91. PMID: 19206510.
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    79. Mobley DL, Dill K. 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.
    80. Mobley DL, Bayly CI, Cooper MD, Dill K. Predictions of hydration free energies from all-atom molecular dynamics simulations. J Phys Chem B. 2009 Apr 09; 113(14):4533-7. PMID: 19271713; PMCID: PMC2684682.
    81. Hribar-Lee B, Vlachy V, Dill K. Modeling Hofmeister Effects. Acta Chim Slov. 2009 Mar 11; 56(1):196-202. PMID: 20161468.
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    82. Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill K. Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations. J Chem Theory Comput. 2009 Feb 10; 5(2):350-358. PMID: 20150953.
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    83. Voelz VA, Shell MS, Dill K. Predicting peptide structures in native proteins from physical simulations of fragments. PLoS Comput Biol. 2009 Feb; 5(2):e1000281. PMID: 19197352; PMCID: PMC2629132.
    84. Shell MS, Ozkan SB, Voelz V, Wu GA, Dill K. Blind test of physics-based prediction of protein structures. Biophys J. 2009 Feb; 96(3):917-24. PMID: 19186130; PMCID: PMC2716649.
    85. MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson MP, Dill K. Assessment of the protein-structure refinement category in CASP8. Proteins. 2009; 77 Suppl 9:66-80. PMID: 19714776; PMCID: PMC2801025.
    86. Watkins GA, Jones EF, Scott Shell M, VanBrocklin HF, Pan MH, Hanrahan SM, Feng JJ, He J, Sounni NE, Dill K, 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.
    87. Wu GA, Coutsias EA, Dill K. Iterative assembly of helical proteins by optimal hydrophobic packing. Structure. 2008 Aug 06; 16(8):1257-66. PMID: 18682227; PMCID: PMC2629734.
    88. Lee BC, Chu TK, Dill K, Zuckermann RN. Biomimetic nanostructures: creating a high-affinity zinc-binding site in a folded nonbiological polymer. J Am Chem Soc. 2008 Jul 09; 130(27):8847-55. PMID: 18597438; PMCID: PMC2748234.
    89. Stock G, Ghosh K, Dill K. Maximum Caliber: a variational approach applied to two-state dynamics. J Chem Phys. 2008 May 21; 128(19):194102. PMID: 18500851; PMCID: PMC2671656.
    90. Shell MS, Ritterson R, Dill K. A test on peptide stability of AMBER force fields with implicit solvation. J Phys Chem B. 2008 Jun 05; 112(22):6878-86. PMID: 18471007; PMCID: PMC2699260.
    91. Mobley DL, Baker JR, Barber AE, Fennell CJ, Dill K. Charge asymmetries in hydration of polar solutes. J Phys Chem B. 2008 Feb 28; 112(8):2405-14. PMID: 18251538; PMCID: PMC2745216.
    92. Urbic T, Urbic T, Avbelj F, Dill K. Molecular Simulations Find Stable Structures in Fragments of Protein G. Acta Chim Slov. 2008 Jan 26; 2008(55):385-395. PMID: 20448839.
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    93. Mobley DL, Dill K, 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.
    94. Dill K, Ozkan SB, Shell MS, Weikl TR. The protein folding problem. Annu Rev Biophys. 2008; 37:289-316. PMID: 18573083; PMCID: PMC2443096.
    95. Ghosh K, Ozkan SB, Dill K. The ultimate speed limit to protein folding is conformational searching. J Am Chem Soc. 2007 Oct 03; 129(39):11920-7. PMID: 17824609.
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    96. Ozkan SB, Wu GA, Chodera JD, Dill K. Protein folding by zipping and assembly. Proc Natl Acad Sci U S A. 2007 Jul 17; 104(29):11987-92. PMID: 17620603; PMCID: PMC1924571.
    97. Dill K, 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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    98. Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill K. 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.
    99. Bradford JA, Dill K. 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.
    100. Chodera JD, Singhal N, Pande VS, Dill K, 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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    101. Lucas A, Huang L, Joshi A, Dill K. 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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    102. Voelz VA, Dill K. Exploring zipping and assembly as a protein folding principle. Proteins. 2007 Mar 01; 66(4):877-88. PMID: 17154424.
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    103. 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 08; 111(9):2288-92. PMID: 17295536; PMCID: PMC3261839.
    104. Mobley DL, Dumont E, Chodera JD, Dill K. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. J Phys Chem B. 2007 Mar 08; 111(9):2242-54. PMID: 17291029.
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    105. Mobley DL, Chodera JD, Dill K. The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change. J Chem Theory Comput. 2007; 3(4):1231-1235. PMID: 18843379.
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    106. Hockenmaier J, Joshi AK, Dill K. Routes are trees: the parsing perspective on protein folding. Proteins. 2007 Jan 01; 66(1):1-15. PMID: 17063473.
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    107. Chodera JD, Swope WC, Pitera JW, Seok C, Dill K. 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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    108. Weikl TR, Dill K. Transition-states in protein folding kinetics: the structural interpretation of Phi values. J Mol Biol. 2007 Feb 02; 365(5):1578-86. PMID: 17141267.
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    109. Mobley DL, Chodera JD, Dill K. 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.
    110. Ho BK, Dill K. Folding very short peptides using molecular dynamics. PLoS Comput Biol. 2006 Apr; 2(4):e27. PMID: 16617376; PMCID: PMC1435986.
    111. Ghosh K, Dill K, Inamdar MM, Seitaridou E, Phillips R. Teaching the principles of statistical dynamics. Am J Phys. 2006 Feb 01; 74(2):123-133. PMID: 23585693.
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    112. Chiang D, Joshi AK, Dill K. 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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    113. Chorny I, Dill K, Jacobson MP. Surfaces affect ion pairing. J Phys Chem B. 2005 Dec 22; 109(50):24056-60. PMID: 16375397.
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    114. Xu H, Dill K. 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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    115. Coutsias EA, Seok C, Dill K. 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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    116. Lee BC, Zuckermann RN, Dill K. 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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    117. Merlo C, Dill K, 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.
    118. Ho BK, Coutsias EA, Seok C, Dill K. The flexibility in the proline ring couples to the protein backbone. Protein Sci. 2005 Apr; 14(4):1011-8. PMID: 15772308; PMCID: PMC2253451.
    119. Jaswal SS, Truhlar SM, Dill K, 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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    120. Dill K, 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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    121. Coutsias EA, Seok C, Dill K. Using quaternions to calculate RMSD. J Comput Chem. 2004 Nov 30; 25(15):1849-57. PMID: 15376254.
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    122. Horn T, Lee BC, Dill K, 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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    123. Weikl TR, Palassini M, Dill K. Cooperativity in two-state protein folding kinetics. Protein Sci. 2004 Mar; 13(3):822-9. PMID: 14978313; PMCID: PMC2286727.
    124. Coutsias EA, Seok C, Jacobson MP, Dill K. A kinematic view of loop closure. J Comput Chem. 2004 Mar; 25(4):510-28. PMID: 14735570.
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    125. Wu CW, Kirshenbaum K, Sanborn TJ, Patch JA, Huang K, Dill K, Zuckermann RN, Barron AE. Structural and spectroscopic studies of peptoid oligomers with alpha-chiral aliphatic side chains. J Am Chem Soc. 2003 Nov 05; 125(44):13525-30. PMID: 14583049.
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    126. Schonbrun J, Dill K. Fast protein folding kinetics. Proc Natl Acad Sci U S A. 2003 Oct 28; 100(22):12678-82. PMID: 14569019; PMCID: PMC240677.
    127. Weikl TR, Dill K. 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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    128. Truskett TM, Dill K. A simple analytical model of water. Biophys Chem. 2003 Sep; 105(2-3):449-59. PMID: 14499910.
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    129. Weikl TR, Dill K. Folding rates and low-entropy-loss routes of two-state proteins. J Mol Biol. 2003 Jun 06; 329(3):585-98. PMID: 12767836.
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    130. Seok C, Rosen JB, Chodera JD, Dill K. 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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    131. Song G, Thomas S, Dill K, 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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    132. Amato NM, Dill K, 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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    133. Ozkan SB, Dill K, Bahar I. Computing the transition state populations in simple protein models. Biopolymers. 2003 Jan; 68(1):35-46. PMID: 12579578.
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    134. Southall NT, Dill K. 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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    135. Hribar B, Southall NT, Vlachy V, Dill K. How ions affect the structure of water. J Am Chem Soc. 2002 Oct 16; 124(41):12302-11. PMID: 12371874; PMCID: PMC1513647.
    136. Ozkan SB, Dill K, 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.
    137. Ball KD, Erman B, Dill K. The elastic net algorithm and protein structure prediction. J Comput Chem. 2002 Jan 15; 23(1):77-83. PMID: 11913391.
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