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Ken Dill, PhD

Title(s)Professor Emeritus, Pharmaceutical Chemistry
SchoolSchool of Pharmacy
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. Wagoner JA, Dill KA. Mechanisms for achieving high speed and efficiency in biomolecular machines. Proc Natl Acad Sci U S A. 2019 Mar 08. PMID: 30850521.
      View in: PubMed
    2. Dixit PD, Dill KA. Building Markov state models using optimal transport theory. J Chem Phys. 2019 Feb 07; 150(5):054105. PMID: 30736685.
      View in: PubMed
    3. Urbic T, Dill KA. Water is a cagey liquid. J Am Chem Soc. 2018 Nov 21. PMID: 30461279.
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    4. Robertson JC, Perez A, Dill KA. MELD × MD Folds Nonthreadables, Giving Native Structures and Populations. J Chem Theory Comput. 2018 Nov 21. PMID: 30407805.
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    5. Ignatov M, Liu C, Alekseenko A, Sun Z, Padhorny D, Kotelnikov S, Kazennov A, Grebenkin I, Kholodov Y, Kolosvari I, Perez A, Dill K, Kozakov D. Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge. J Comput Aided Mol Des. 2018 Nov 12. PMID: 30421350.
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    6. Agozzino L, Dill KA. Protein evolution speed depends on its stability and abundance and on chaperone concentrations. Proc Natl Acad Sci U S A. 2018 09 11; 115(37):9092-9097. PMID: 30150386.
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    7. Santra M, Dill KA, de Graff AMR. How Do Chaperones Protect a Cell's Proteins from Oxidative Damage? Cell Syst. 2018 Jun 27; 6(6):743-751.e3. PMID: 29886110.
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    8. Dill KA. Selected Publications of Ken A. Dill. J Phys Chem B. 2018 May 31; 122(21):5269-5277. PMID: 29847954.
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    9. Dill KA. Autobiography of Ken A. Dill. J Phys Chem B. 2018 May 31; 122(21):5263-5266. PMID: 29847956.
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    10. Dill KA. Colleagues of Ken A. Dill. J Phys Chem B. 2018 May 31; 122(21):5267-5268. PMID: 29847955.
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    11. 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
    12. Dixit PD, Dill KA. Caliber Corrected Markov Modeling (C2M2): Correcting Equilibrium Markov Models. J Chem Theory Comput. 2018 Feb 13; 14(2):1111-1119. PMID: 29323898.
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    13. Dixit PD, Wagoner J, Weistuch C, Pressé S, Ghosh K, Dill KA. Perspective: Maximum caliber is a general variational principle for dynamical systems. J Chem Phys. 2018 Jan 07; 148(1):010901. PMID: 29306272.
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    14. Brini E, Fennell CJ, Fernandez-Serra M, Hribar-Lee B, Lukšic M, Dill KA. 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
    15. Urbic T, Dill KA. Analytical theory of the hydrophobic effect of solutes in water. Phys Rev E. 2017 Sep; 96(3-1):032101. PMID: 29347026.
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    16. Guseva E, Zuckermann RN, Dill KA. Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers. Proc Natl Acad Sci U S A. 2017 09 05; 114(36):E7460-E7468. PMID: 28831002.
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    17. Szenk M, Dill KA, 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
    18. Perez A, Morrone JA, Dill KA. 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
    19. Santra M, Farrell DW, Dill KA. Bacterial proteostasis balances energy and chaperone utilization efficiently. Proc Natl Acad Sci U S A. 2017 03 28; 114(13):E2654-E2661. PMID: 28292901.
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    20. Morrone JA, Perez A, Deng Q, Ha SN, Holloway MK, Sawyer TK, Sherborne BS, Brown FK, Dill KA. 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.
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    21. Morrone JA, Perez A, MacCallum J, Dill KA. Computed Binding of Peptides to Proteins with MELD-Accelerated Molecular Dynamics. J Chem Theory Comput. 2017 Feb 14; 13(2):870-876. PMID: 28042966.
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    22. Perez A, Morrone JA, Brini E, MacCallum JL, Dill KA. Blind protein structure prediction using accelerated free-energy simulations. Sci Adv. 2016 Nov; 2(11):e1601274. PMID: 27847872.
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    23. Brini E, Paranahewage SS, Fennell CJ, Dill KA. Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules. J Comput Aided Mol Des. 2016 11; 30(11):1067-1077. PMID: 27632227.
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    24. Ghosh K, de Graff AM, Sawle L, Dill KA. Role of Proteome Physical Chemistry in Cell Behavior. J Phys Chem B. 2016 09 15; 120(36):9549-63. PMID: 27513457.
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    25. Wagoner JA, Dill KA. Molecular Motors: Power Strokes Outperform Brownian Ratchets. J Phys Chem B. 2016 07 07; 120(26):6327-36. PMID: 27136319.
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    26. Maitra A, Dill KA. 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].
    27. 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; PMCID: PMC4785060 [Available on 02/01/17].
    28. 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; PMCID: PMC4684272 [Available on 12/28/16].
    29. 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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    30. de Graff AM, Hazoglou MJ, Dill KA. Highly Charged Proteins: The Achilles' Heel of Aging Proteomes. Structure. 2016 Feb 02; 24(2):329-36. PMID: 26724998.
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    31. 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.
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    32. 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; PMCID: PMC4813323 [Available on 10/13/16].
    33. 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.
    34. 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 07; 143(5):051104. PMID: 26254635.
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    35. 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 02; 112(22):6985-90. PMID: 26038552; PMCID: PMC4460504.
    36. 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.
    37. 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; PMCID: PMC4675652.
    38. 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.
    39. 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.
    40. 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.
    41. 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.
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    42. 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.
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    43. Drechsel NJ, Fennell CJ, Dill KA, 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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    44. 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.
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    45. 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.
    46. Dixit PD, Dill KA. 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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    47. 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.
    48. 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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    49. 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.
    50. Roy A, Perez A, Dill KA, 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.
    51. 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.
    52. 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.
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    53. 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 01; 111(18):180604. PMID: 24237501.
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    54. 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.
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    55. Rocklin GJ, Mobley DL, Dill KA. 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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    56. 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.
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    57. 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.
    58. 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.
    59. Dill KA. Biophysics. Introduction. Annu Rev Biophys. 2013; 42. PMID: 23798065.
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    60. 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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    61. Perez A, Yang Z, Bahar I, Dill KA, 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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    62. 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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    63. 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 04; 109(36):14320-5. PMID: 22908242; PMCID: PMC3437879.
    64. 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.
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    65. 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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    66. 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.
    67. Schmit JD, Dill K. Growth rates of protein crystals. J Am Chem Soc. 2012 Mar 07; 134(9):3934-7. PMID: 22339624; PMCID: PMC3311159.
    68. 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.
    69. 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.
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    70. Dill KA, 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.
    71. Fennell CJ, Dill KA. Physical Modeling of Aqueous Solvation. J Stat Phys. 2011 Oct 01; 145(2):209-226. PMID: 25143658.
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    72. 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.
    73. 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.
    74. 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.
    75. 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.
    76. 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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    77. 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.
    78. 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.
    79. 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.
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    80. 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.
    81. 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.
    82. Schmit JD, Dill KA. The stabilities of protein crystals. J Phys Chem B. 2010 Mar 25; 114(11):4020-7. PMID: 20199035.
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    83. 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.
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    84. 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.
    85. 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.
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    86. 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.
    87. 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.
    88. 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.
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    89. 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.
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    90. 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 09; 113(14):4533-7. PMID: 19271713.
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    91. Hribar-Lee B, Vlachy V, Dill KA. Modeling Hofmeister Effects. Acta Chim Slov. 2009 Mar 11; 56(1):196-202. PMID: 20161468.
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    92. Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. 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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    93. 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.
    94. 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.
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    95. 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.
    96. 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.
    97. Wu GA, Coutsias EA, Dill KA. Iterative assembly of helical proteins by optimal hydrophobic packing. Structure. 2008 Aug 06; 16(8):1257-66. PMID: 18682227; PMCID: PMC2629734.
    98. 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 09; 130(27):8847-55. PMID: 18597438; PMCID: PMC2748234.
    99. 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.
    100. Shell MS, Ritterson R, Dill KA. 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.
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    101. 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.
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    102. Urbic T, Urbic T, Avbelj F, Dill KA. 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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    103. 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.
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    104. Dill KA, Ozkan SB, Shell MS, Weikl TR. The protein folding problem. Annu Rev Biophys. 2008; 37:289-316. PMID: 18573083; PMCID: PMC2443096.
    105. Ghosh K, Ozkan SB, Dill KA. 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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    106. 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.
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    107. 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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    108. 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.
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    109. 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.
    110. 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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    111. 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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    112. Voelz VA, Dill KA. Exploring zipping and assembly as a protein folding principle. Proteins. 2007 Mar 01; 66(4):877-88. PMID: 17154424.
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    113. 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.
    114. 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 08; 111(9):2242-54. PMID: 17291029.
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    115. Mobley DL, Chodera JD, Dill KA. 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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    116. Hockenmaier J, Joshi AK, Dill KA. Routes are trees: the parsing perspective on protein folding. Proteins. 2007 Jan 01; 66(1):1-15. PMID: 17063473.
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    117. 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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    118. Weikl TR, Dill KA. 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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    119. 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.
    120. Ho BK, Dill KA. Folding very short peptides using molecular dynamics. PLoS Comput Biol. 2006 Apr; 2(4):e27. PMID: 16617376; PMCID: PMC1435986.
    121. Ghosh K, Dill KA, 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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    122. 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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    123. 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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    124. 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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    125. 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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    126. 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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    127. 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.
    128. 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.
    129. 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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    130. 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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    131. 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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    132. 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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    133. 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.
    134. 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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    135. 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 05; 125(44):13525-30. PMID: 14583049.
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    136. 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.
    137. 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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    138. 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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    139. Weikl TR, Dill KA. 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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    140. 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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    141. 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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    142. 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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    143. 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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    144. 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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    145. 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.
    146. 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.
    147. 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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