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Ken Dill, PhD

Title(s)Professor Emeritus, Pharmaceutical Chemistry
SchoolSchool of Pharmacy
AddressLocation Required
Varies CA 00000
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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Computing Ligands Bound to Proteins Using MELD-Accelerated MD. J Chem Theory Comput. 2020 Sep 23. Liu C, Brini E, Perez A, Dill KA. PMID: 32910647.
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    2. How Do Cells Adapt? Stories Told in Landscapes. Annu Rev Chem Biomol Eng. 2020 Jun 07; 11:155-182. Agozzino L, Balázsi G, Wang J, Dill KA. PMID: 32513086.
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    3. ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking. Proteins. 2020 08; 88(8):1082-1090. Padhorny D, Porter KA, Ignatov M, Alekseenko A, Beglov D, Kotelnikov S, Ashizawa R, Desta I, Alam N, Sun Z, Brini E, Dill K, Schueler-Furman O, Vajda S, Kozakov D. PMID: 32142178.
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    4. Diet modulates brain network stability, a biomarker for brain aging, in young adults. Proc Natl Acad Sci U S A. 2020 03 17; 117(11):6170-6177. Mujica-Parodi LR, Amgalan A, Sultan SF, Antal B, Sun X, Skiena S, Lithen A, Adra N, Ratai EM, Weistuch C, Govindarajan ST, Strey HH, Dill KA, Stufflebeam SM, Veech RL, Clarke K. PMID: 32127481.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
    5. The Maximum Caliber Variational Principle for Nonequilibria. Annu Rev Phys Chem. 2020 Apr 20; 71:213-238. Ghosh K, Dixit PD, Agozzino L, Dill KA. PMID: 32075515.
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    6. Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45. Proteins. 2020 08; 88(8):1037-1049. Khramushin A, Marcu O, Alam N, Shimony O, Padhorny D, Brini E, Dill KA, Vajda S, Kozakov D, Schueler-Furman O. PMID: 31891416.
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    7. Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4. J Comput Aided Mol Des. 2020 02; 34(2):179-189. Kotelnikov S, Alekseenko A, Liu C, Ignatov M, Padhorny D, Brini E, Lukin M, Coutsias E, Dill KA, Kozakov D. PMID: 31879831.
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    8. Opposing Pressures of Speed and Efficiency Guide the Evolution of Molecular Machines. Mol Biol Evol. 2019 12 01; 36(12):2813-2822. Wagoner JA, Dill KA. PMID: 31432071.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    9. Proteostasis collapse is a driver of cell aging and death. Proc Natl Acad Sci U S A. 2019 10 29; 116(44):22173-22178. Santra M, Dill KA, de Graff AMR. PMID: 31619571.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsCells
    10. NMR-assisted protein structure prediction with MELDxMD. Proteins. 2019 12; 87(12):1333-1340. Robertson JC, Nassar R, Liu C, Brini E, Dill KA, Perez A. PMID: 31350773.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    11. Minimal constraints for maximum caliber analysis of dissipative steady-state systems. Phys Rev E. 2019 Jul; 100(1-1):010105. Agozzino L, Dill K. PMID: 31499924.
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    12. Predicting Protein Dimer Structures Using MELD × MD. J Chem Theory Comput. 2019 May 14; 15(5):3381-3389. Brini E, Kozakov D, Dill KA. PMID: 30908034.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    13. Mechanisms for achieving high speed and efficiency in biomolecular machines. Proc Natl Acad Sci U S A. 2019 03 26; 116(13):5902-5907. Wagoner JA, Dill KA. PMID: 30850521.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    14. Building Markov state models using optimal transport theory. J Chem Phys. 2019 Feb 07; 150(5):054105. Dixit PD, Dill KA. PMID: 30736685.
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    15. Water Is a Cagey Liquid. J Am Chem Soc. 2018 12 12; 140(49):17106-17113. Urbic T, Dill KA. PMID: 30461279.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    16. MELD × MD Folds Nonthreadables, Giving Native Structures and Populations. J Chem Theory Comput. 2018 Dec 11; 14(12):6734-6740. Robertson JC, Perez A, Dill KA. PMID: 30407805.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    17. 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. 2019 01; 33(1):119-127. 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. PMID: 30421350.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    18. Hierarchy of anomalies in the two-dimensional Mercedes-Benz model of water. Phys Rev E. 2018 Sep; 98(3). Urbic T, Dill KA. PMID: 32025599.
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    19. 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. Agozzino L, Dill KA. PMID: 30150386.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    20. How Do Chaperones Protect a Cell's Proteins from Oxidative Damage? Cell Syst. 2018 06 27; 6(6):743-751.e3. Santra M, Dill KA, de Graff AMR. PMID: 29886110.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    21. Selected Publications of Ken A. Dill. J Phys Chem B. 2018 05 31; 122(21):5269-5277. Dill KA. PMID: 29847954.
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    22. Colleagues of Ken A. Dill. J Phys Chem B. 2018 05 31; 122(21):5267-5268. Dill KA. PMID: 29847955.
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    23. Autobiography of Ken A. Dill. J Phys Chem B. 2018 05 31; 122(21):5263-5266. Dill KA. PMID: 29847956.
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    24. MELD-Path Efficiently Computes Conformational Transitions, Including Multiple and Diverse Paths. J Chem Theory Comput. 2018 Apr 10; 14(4):2109-2116. Perez A, Sittel F, Stock G, Dill K. PMID: 29547695.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    25. Caliber Corrected Markov Modeling (C2M2): Correcting Equilibrium Markov Models. J Chem Theory Comput. 2018 Feb 13; 14(2):1111-1119. Dixit PD, Dill KA. PMID: 29323898.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    26. Perspective: Maximum caliber is a general variational principle for dynamical systems. J Chem Phys. 2018 Jan 07; 148(1):010901. Dixit PD, Wagoner J, Weistuch C, Pressé S, Ghosh K, Dill KA. PMID: 29306272.
      View in: PubMed   Mentions: 2     Fields:    
    27. Controlling the viscosities of antibody solutions through control of their binding sites. J Mol Liq. 2018 Nov 15; 270:234-242. Kastelic M, Dill KA, Kalyuzhnyi YV, Vlachy V. PMID: 30906093.
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    28. How Water's Properties Are Encoded in Its Molecular Structure and Energies. Chem Rev. 2017 Oct 11; 117(19):12385-12414. Brini E, Fennell CJ, Fernandez-Serra M, Hribar-Lee B, Lukšic M, Dill KA. PMID: 28949513.
      View in: PubMed   Mentions: 9     Fields:    
    29. Analytical theory of the hydrophobic effect of solutes in water. Phys Rev E. 2017 Sep; 96(3-1):032101. Urbic T, Dill KA. PMID: 29347026.
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    30. 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. Guseva E, Zuckermann RN, Dill KA. PMID: 28831002.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    31. Why Do Fast-Growing Bacteria Enter Overflow Metabolism? Testing the Membrane Real Estate Hypothesis. Cell Syst. 2017 08 23; 5(2):95-104. Szenk M, Dill KA, de Graff AMR. PMID: 28755958.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    32. Accelerating physical simulations of proteins by leveraging external knowledge. Wiley Interdiscip Rev Comput Mol Sci. 2017 Sep-Oct; 7(5). Perez A, Morrone JA, Dill KA. PMID: 28959358.
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    33. Bacterial proteostasis balances energy and chaperone utilization efficiently. Proc Natl Acad Sci U S A. 2017 03 28; 114(13):E2654-E2661. Santra M, Farrell DW, Dill KA. PMID: 28292901.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    34. 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. Morrone JA, Perez A, Deng Q, Ha SN, Holloway MK, Sawyer TK, Sherborne BS, Brown FK, Dill KA. PMID: 28042965.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    35. Computed Binding of Peptides to Proteins with MELD-Accelerated Molecular Dynamics. J Chem Theory Comput. 2017 Feb 14; 13(2):870-876. Morrone JA, Perez A, MacCallum J, Dill KA. PMID: 28042966.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    36. Blind protein structure prediction using accelerated free-energy simulations. Sci Adv. 2016 Nov; 2(11):e1601274. Perez A, Morrone JA, Brini E, MacCallum JL, Dill KA. PMID: 27847872.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    37. 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. Brini E, Paranahewage SS, Fennell CJ, Dill KA. PMID: 27632227.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    38. Role of Proteome Physical Chemistry in Cell Behavior. J Phys Chem B. 2016 09 15; 120(36):9549-63. Ghosh K, de Graff AM, Sawle L, Dill KA. PMID: 27513457.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    39. Molecular Motors: Power Strokes Outperform Brownian Ratchets. J Phys Chem B. 2016 07 07; 120(26):6327-36. Wagoner JA, Dill KA. PMID: 27136319.
      View in: PubMed   Mentions: 7     Fields:    
    40. Modeling the Overproduction of Ribosomes when Antibacterial Drugs Act on Cells. Biophys J. 2016 Feb 02; 110(3):743-748. Maitra A, Dill KA. PMID: 26840738.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    41. Advances in free-energy-based simulations of protein folding and ligand binding. Curr Opin Struct Biol. 2016 Feb; 36:25-31. Perez A, Morrone JA, Simmerling C, Dill KA. PMID: 26773233.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    42. Constraint methods that accelerate free-energy simulations of biomolecules. J Chem Phys. 2015 Dec 28; 143(24):243143. Perez A, MacCallum JL, Coutsias EA, Dill KA. PMID: 26723628.
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    43. Preface: Special Topic on Coarse Graining of Macromolecules, Biopolymers, and Membranes. J Chem Phys. 2015 Dec 28; 143(24):242901. Holm C, Gompper G, Dill KA. PMID: 26723585.
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    44. Highly Charged Proteins: The Achilles' Heel of Aging Proteomes. Structure. 2016 Feb 02; 24(2):329-36. de Graff AM, Hazoglou MJ, Dill KA. PMID: 26724998.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    45. Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes. J Chem Theory Comput. 2015 Nov 10; 11(11):5464-72. Dixit PD, Jain A, Stock G, Dill KA. PMID: 26574334.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    46. 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. Perez A, MacCallum JL, Brini E, Simmerling C, Dill KA. PMID: 26574266.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    47. 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. Perez A, MacCallum JL, Dill KA. PMID: 26351667.
      View in: PubMed   Mentions: 16     Fields:    Translation:Cells
    48. Communication: Maximum caliber is a general variational principle for nonequilibrium statistical mechanics. J Chem Phys. 2015 Aug 07; 143(5):051104. Hazoglou MJ, Walther V, Dixit PD, Dill KA. PMID: 26254635.
      View in: PubMed   Mentions: 2     Fields:    
    49. 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. MacCallum JL, Perez A, Dill KA. PMID: 26038552.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    50. Protein aggregation in salt solutions. Proc Natl Acad Sci U S A. 2015 May 26; 112(21):6766-70. Kastelic M, Kalyuzhnyi YV, Hribar-Lee B, Dill KA, Vlachy V. PMID: 25964322.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    51. 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. Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. PMID: 26579779.
      View in: PubMed   Mentions: 2     Fields:    
    52. Bacterial growth laws reflect the evolutionary importance of energy efficiency. Proc Natl Acad Sci U S A. 2015 Jan 13; 112(2):406-11. Maitra A, Dill KA. PMID: 25548180.
      View in: PubMed   Mentions: 31     Fields:    Translation:Cells
    53. 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. 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. PMID: 25512516.
      View in: PubMed   Mentions: 32     Fields:    Translation:HumansAnimalsCells
    54. 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. Li L, Fennell CJ, Dill KA. PMID: 25494789.
      View in: PubMed   Mentions: 1     Fields:    
    55. Modeling the solvation of nonpolar amino acids in guanidinium chloride solutions. J Phys Chem B. 2014 Sep 11; 118(36):10618-23. Cohen P, Dill KA, Jaswal SS. PMID: 25141127.
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    56. General mechanism of two-state protein folding kinetics. J Am Chem Soc. 2014 Aug 13; 136(32):11420-7. Rollins GC, Dill KA. PMID: 25056406.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    57. TRIFORCE: Tessellated Semianalytical Solvent Exposed Surface Areas and Derivatives. J Chem Theory Comput. 2014 Sep 09; 10(9):4121-4132. Drechsel NJ, Fennell CJ, Dill KA, Villà-Freixa J. PMID: 25221446.
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    58. Extracting representative structures from protein conformational ensembles. Proteins. 2014 Oct; 82(10):2671-80. Perez A, Roy A, Kasavajhala K, Wagaman A, Dill KA, MacCallum JL. PMID: 24975328.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    59. Single molecule conformational memory extraction: p5ab RNA hairpin. J Phys Chem B. 2014 Jun 19; 118(24):6597-603. Pressé S, Peterson J, Lee J, Elms P, MacCallum JL, Marqusee S, Bustamante C, Dill K. PMID: 24898871.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    60. Inferring Microscopic Kinetic Rates from Stationary State Distributions. J Chem Theory Comput. 2014 Aug 12; 10(8):3002-3005. Dixit PD, Dill KA. PMID: 25136269.
      View in: PubMed   Mentions: 2     Fields:    
    61. Using interpolation for fast and accurate calculation of ion-ion interactions. J Phys Chem B. 2014 Jul 17; 118(28):8017-25. Lukšic M, Fennell CJ, Dill KA. PMID: 24625086.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    62. Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge. J Comput Aided Mol Des. 2014 Mar; 28(3):259-64. Li L, Dill KA, Fennell CJ. PMID: 24474161.
      View in: PubMed   Mentions: 6     Fields:    
    63. 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. Li L, Fennell CJ, Dill KA. PMID: 24299013.
      View in: PubMed   Mentions: 12     Fields:    
    64. Computing the relative stabilities and the per-residue components in protein conformational changes. Structure. 2014 Jan 07; 22(1):168-75. Roy A, Perez A, Dill KA, Maccallum JL. PMID: 24316402.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    65. A maximum entropy framework for nonexponential distributions. Proc Natl Acad Sci U S A. 2013 Dec 17; 110(51):20380-5. Peterson J, Dixit PD, Dill KA. PMID: 24297895.
      View in: PubMed   Mentions: 5     Fields:    
    66. 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. Rocklin GJ, Mobley DL, Dill KA, Hünenberger PH. PMID: 24320250.
      View in: PubMed   Mentions: 42     Fields:    Translation:AnimalsCells
    67. Nonadditive entropies yield probability distributions with biases not warranted by the data. Phys Rev Lett. 2013 Nov 01; 111(18):180604. Pressé S, Ghosh K, Lee J, Dill KA. PMID: 24237501.
      View in: PubMed   Mentions: 1     Fields:    
    68. Blind prediction of charged ligand binding affinities in a model binding site. J Mol Biol. 2013 Nov 15; 425(22):4569-83. Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA. PMID: 23896298.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    69. 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. Rocklin GJ, Mobley DL, Dill KA. PMID: 24015114.
      View in: PubMed   Mentions: 8     Fields:    
    70. Separated topologies--a method for relative binding free energy calculations using orientational restraints. J Chem Phys. 2013 Feb 28; 138(8):085104. Rocklin GJ, Mobley DL, Dill KA. PMID: 23464180.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    71. Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations. MAbs. 2013 Mar-Apr; 5(2):306-22. Kortkhonjia E, Brandman R, Zhou JZ, Voelz VA, Chorny I, Kabakoff B, Patapoff TW, Dill KA, Swartz TE. PMID: 23396076.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    72. Extracting conformational memory from single-molecule kinetic data. J Phys Chem B. 2013 Jan 17; 117(2):495-502. Pressé S, Lee J, Dill KA. PMID: 23259771.
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    73. Biophysics. Introduction. Annu Rev Biophys. 2013; 42. Dill KA. PMID: 23798065.
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    74. The protein-folding problem, 50 years on. Science. 2012 Nov 23; 338(6110):1042-6. Dill KA, MacCallum JL. PMID: 23180855.
      View in: PubMed   Mentions: 227     Fields:    Translation:Cells
    75. FlexE: Using elastic network models to compare models of protein structure. J Chem Theory Comput. 2012 Oct 09; 8(10):3985-3991. Perez A, Yang Z, Bahar I, Dill KA, MacCallum JL. PMID: 25530735.
      View in: PubMed   Mentions: 6     Fields:    
    76. A microscopic theory of solvation of monoions. Acta Chim Slov. 2012 Sep; 59(3):554-8. Urbic T, Fennell CJ, Dill KA. PMID: 24061310.
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    77. 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. Butterfoss GL, Yoo B, Jaworski JN, Chorny I, Dill KA, Zuckermann RN, Bonneau R, Kirshenbaum K, Voelz VA. PMID: 22908242.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    78. Simulated evolution of protein-protein interaction networks with realistic topology. PLoS One. 2012; 7(6):e39052. Peterson GJ, Pressé S, Peterson KS, Dill KA. PMID: 22768057.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimals
    79. Simple model of hydrophobic hydration. J Phys Chem B. 2012 May 31; 116(21):6177-86. Lukšic M, Urbic T, Hribar-Lee B, Dill KA. PMID: 22564051.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    80. Simple liquid models with corrected dielectric constants. J Phys Chem B. 2012 Jun 14; 116(23):6936-44. Fennell CJ, Li L, Dill KA. PMID: 22397577.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    81. Growth rates of protein crystals. J Am Chem Soc. 2012 Mar 07; 134(9):3934-7. Schmit JD, Dill K. PMID: 22339624.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    82. Markov processes follow from the principle of maximum caliber. J Chem Phys. 2012 Feb 14; 136(6):064108. Ge H, Pressé S, Ghosh K, Dill KA. PMID: 22360170.
      View in: PubMed   Mentions: 8     Fields:    
    83. Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test. J Comput Aided Mol Des. 2012 May; 26(5):563-8. Kehoe CW, Fennell CJ, Dill KA. PMID: 22205387.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    84. Physical limits of cells and proteomes. Proc Natl Acad Sci U S A. 2011 Nov 01; 108(44):17876-82. Dill KA, Ghosh K, Schmit JD. PMID: 22006304.
      View in: PubMed   Mentions: 73     Fields:    Translation:Cells
    85. Physical Modeling of Aqueous Solvation. J Stat Phys. 2011 Oct 01; 145(2):209-226. Fennell CJ, Dill KA. PMID: 25143658.
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    86. Assessment of protein structure refinement in CASP9. Proteins. 2011; 79 Suppl 10:74-90. MacCallum JL, Pérez A, Schnieders MJ, Hua L, Jacobson MP, Dill KA. PMID: 22069034.
      View in: PubMed   Mentions: 48     Fields:    Translation:Cells
    87. Electrostatics and aggregation: how charge can turn a crystal into a gel. J Chem Phys. 2011 Aug 28; 135(8):085103. Schmit JD, Whitelam S, Dill K. PMID: 21895221.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    88. Modeling aqueous solvation with semi-explicit assembly. Proc Natl Acad Sci U S A. 2011 Feb 22; 108(8):3234-9. Fennell CJ, Kehoe CW, Dill KA. PMID: 21300905.
      View in: PubMed   Mentions: 32     Fields:    
    89. What drives amyloid molecules to assemble into oligomers and fibrils? Biophys J. 2011 Jan 19; 100(2):450-8. Schmit JD, Ghosh K, Dill K. PMID: 21244841.
      View in: PubMed   Mentions: 32     Fields:    Translation:Cells
    90. Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER. Biopolymers. 2011; 96(5):639-50. Voelz VA, Dill KA, Chorny I. PMID: 21184487.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    91. Cellular proteomes have broad distributions of protein stability. Biophys J. 2010 Dec 15; 99(12):3996-4002. Ghosh K, Dill K. PMID: 21156142.
      View in: PubMed   Mentions: 23     Fields:    Translation:AnimalsCells
    92. Receptacle model of salting-in by tetramethylammonium ions. J Phys Chem B. 2010 Nov 25; 114(46):15085-91. Hribar-Lee B, Dill KA, Vlachy V. PMID: 21028768.
      View in: PubMed   Mentions: 1     Fields:    
    93. 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. Peterson GJ, Pressé S, Dill KA. PMID: 20805513.
      View in: PubMed   Mentions: 16     Fields:    
    94. A statistical mechanical theory for a two-dimensional model of water. J Chem Phys. 2010 Jun 14; 132(22):224507. Urbic T, Dill KA. PMID: 20550408.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    95. 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. Kalyuzhnyi YV, Vlachy V, Dill KA. PMID: 20405084.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    96. The stabilities of protein crystals. J Phys Chem B. 2010 Mar 25; 114(11):4020-7. Schmit JD, Dill KA. PMID: 20199035.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    97. Oil/water transfer is partly driven by molecular shape, not just size. J Am Chem Soc. 2010 Jan 13; 132(1):234-40. Fennell CJ, Kehoe C, Dill KA. PMID: 19961159.
      View in: PubMed   Mentions: 21     Fields:    
    98. Theory for the three-dimensional Mercedes-Benz model of water. J Chem Phys. 2009 Nov 21; 131(19):194504. Bizjak A, Urbic T, Vlachy V, Dill KA. PMID: 19929057.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    99. 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. Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill KA, Shoichet BK. PMID: 19782087.
      View in: PubMed   Mentions: 70     Fields:    Translation:Cells
    100. Trajectory approach to two-state kinetics of single particles on sculpted energy landscapes. Phys Rev Lett. 2009 Jul 31; 103(5):050603. Wu D, Ghosh K, Inamdar M, Lee HJ, Fraser S, Dill K, Phillips R. PMID: 19792475.
      View in: PubMed   Mentions: 4     Fields:    
    101. Computing protein stabilities from their chain lengths. Proc Natl Acad Sci U S A. 2009 Jun 30; 106(26):10649-54. Ghosh K, Dill KA. PMID: 19541647.
      View in: PubMed   Mentions: 32     Fields:    Translation:Cells
    102. Ion pairing in molecular simulations of aqueous alkali halide solutions. J Phys Chem B. 2009 May 14; 113(19):6782-91. Fennell CJ, Bizjak A, Vlachy V, Dill KA. PMID: 19206510.
      View in: PubMed   Mentions: 24     Fields:    
    103. Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Structure. 2009 Apr 15; 17(4):489-98. Mobley DL, Dill KA. PMID: 19368882.
      View in: PubMed   Mentions: 165     Fields:    Translation:Cells
    104. Predictions of hydration free energies from all-atom molecular dynamics simulations. J Phys Chem B. 2009 Apr 09; 113(14):4533-7. Mobley DL, Bayly CI, Cooper MD, Dill KA. PMID: 19271713.
      View in: PubMed   Mentions: 31     Fields:    
    105. Modeling Hofmeister Effects. Acta Chim Slov. 2009 Mar 11; 56(1):196-202. Hribar-Lee B, Vlachy V, Dill KA. PMID: 20161468.
      View in: PubMed   Mentions: 2     Fields:    
    106. 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. Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. PMID: 20150953.
      View in: PubMed   Mentions: 104     Fields:    
    107. Predicting peptide structures in native proteins from physical simulations of fragments. PLoS Comput Biol. 2009 Feb; 5(2):e1000281. Voelz VA, Shell MS, Dill KA. PMID: 19197352.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    108. Blind test of physics-based prediction of protein structures. Biophys J. 2009 Feb; 96(3):917-24. Shell MS, Ozkan SB, Voelz V, Wu GA, Dill KA. PMID: 19186130.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    109. Assessment of the protein-structure refinement category in CASP8. Proteins. 2009; 77 Suppl 9:66-80. MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson MP, Dill KA. PMID: 19714776.
      View in: PubMed   Mentions: 35     Fields:    Translation:Cells
    110. Development of an optimized activatable MMP-14 targeted SPECT imaging probe. Bioorg Med Chem. 2009 Jan 15; 17(2):653-9. 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. PMID: 19109023.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansCells
    111. Iterative assembly of helical proteins by optimal hydrophobic packing. Structure. 2008 Aug 06; 16(8):1257-66. Wu GA, Coutsias EA, Dill KA. PMID: 18682227.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    112. 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. Lee BC, Chu TK, Dill KA, Zuckermann RN. PMID: 18597438.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    113. Maximum Caliber: a variational approach applied to two-state dynamics. J Chem Phys. 2008 May 21; 128(19):194102. Stock G, Ghosh K, Dill KA. PMID: 18500851.
      View in: PubMed   Mentions: 12     Fields:    
    114. A test on peptide stability of AMBER force fields with implicit solvation. J Phys Chem B. 2008 Jun 05; 112(22):6878-86. Shell MS, Ritterson R, Dill KA. PMID: 18471007.
      View in: PubMed   Mentions: 32     Fields:    Translation:Cells
    115. Charge asymmetries in hydration of polar solutes. J Phys Chem B. 2008 Feb 28; 112(8):2405-14. Mobley DL, Baker JR, Barber AE, Fennell CJ, Dill KA. PMID: 18251538.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    116. Molecular Simulations Find Stable Structures in Fragments of Protein G. Acta Chim Slov. 2008 Jan 26; 2008(55):385-395. Urbic T, Urbic T, Avbelj F, Dill KA. PMID: 20448839.
      View in: PubMed   Mentions:    Fields:    
    117. Treating entropy and conformational changes in implicit solvent simulations of small molecules. J Phys Chem B. 2008 Jan 24; 112(3):938-46. Mobley DL, Dill KA, Chodera JD. PMID: 18171044.
      View in: PubMed   Mentions: 39     Fields:    Translation:Cells
    118. The protein folding problem. Annu Rev Biophys. 2008; 37:289-316. Dill KA, Ozkan SB, Shell MS, Weikl TR. PMID: 18573083.
      View in: PubMed   Mentions: 209     Fields:    Translation:Cells
    119. The ultimate speed limit to protein folding is conformational searching. J Am Chem Soc. 2007 Oct 03; 129(39):11920-7. Ghosh K, Ozkan SB, Dill KA. PMID: 17824609.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    120. Protein folding by zipping and assembly. Proc Natl Acad Sci U S A. 2007 Jul 17; 104(29):11987-92. Ozkan SB, Wu GA, Chodera JD, Dill KA. PMID: 17620603.
      View in: PubMed   Mentions: 59     Fields:    Translation:Cells
    121. The protein folding problem: when will it be solved? Curr Opin Struct Biol. 2007 Jun; 17(3):342-6. Dill KA, Ozkan SB, Weikl TR, Chodera JD, Voelz VA. PMID: 17572080.
      View in: PubMed   Mentions: 50     Fields:    Translation:HumansAnimalsCells
    122. Predicting absolute ligand binding free energies to a simple model site. J Mol Biol. 2007 Aug 24; 371(4):1118-34. Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA. PMID: 17599350.
      View in: PubMed   Mentions: 102     Fields:    Translation:Cells
    123. 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. Bradford JA, Dill KA. PMID: 17548812.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    124. Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. J Chem Phys. 2007 Apr 21; 126(15):155101. Chodera JD, Singhal N, Pande VS, Dill KA, Swope WC. PMID: 17461665.
      View in: PubMed   Mentions: 144     Fields:    Translation:Cells
    125. Statistical mechanics of helix bundles using a dynamic programming approach. J Am Chem Soc. 2007 Apr 11; 129(14):4272-81. Lucas A, Huang L, Joshi A, Dill KA. PMID: 17362002.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    126. Exploring zipping and assembly as a protein folding principle. Proteins. 2007 Mar 01; 66(4):877-88. Voelz VA, Dill KA. PMID: 17154424.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    127. Measuring flux distributions for diffusion in the small-numbers limit. J Phys Chem B. 2007 Mar 08; 111(9):2288-92. Seitaridou E, Inamdar MM, Phillips R, Ghosh K, Dill K. PMID: 17295536.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    128. 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. Mobley DL, Dumont E, Chodera JD, Dill KA. PMID: 17291029.
      View in: PubMed   Mentions: 80     Fields:    Translation:Cells
    129. Routes are trees: the parsing perspective on protein folding. Proteins. 2007 Jan 01; 66(1):1-15. Hockenmaier J, Joshi AK, Dill KA. PMID: 17063473.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    130. 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. Mobley DL, Chodera JD, Dill KA. PMID: 18843379.
      View in: PubMed   Mentions: 73     Fields:    
    131. 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. Chodera JD, Swope WC, Pitera JW, Seok C, Dill KA. PMID: 26627148.
      View in: PubMed   Mentions: 100     Fields:    
    132. Transition-states in protein folding kinetics: the structural interpretation of Phi values. J Mol Biol. 2007 Feb 02; 365(5):1578-86. Weikl TR, Dill KA. PMID: 17141267.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    133. On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. J Chem Phys. 2006 Aug 28; 125(8):084902. Mobley DL, Chodera JD, Dill KA. PMID: 16965052.
      View in: PubMed   Mentions: 81     Fields:    Translation:Cells
    134. Folding very short peptides using molecular dynamics. PLoS Comput Biol. 2006 Apr; 2(4):e27. Ho BK, Dill KA. PMID: 16617376.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    135. Teaching the principles of statistical dynamics. Am J Phys. 2006 Feb 01; 74(2):123-133. Ghosh K, Dill KA, Inamdar MM, Seitaridou E, Phillips R. PMID: 23585693.
      View in: PubMed   Mentions:
    136. A grammatical theory for the conformational changes of simple helix bundles. J Comput Biol. 2006 Jan-Feb; 13(1):21-42. Chiang D, Joshi AK, Dill KA. PMID: 16472020.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    137. Surfaces affect ion pairing. J Phys Chem B. 2005 Dec 22; 109(50):24056-60. Chorny I, Dill KA, Jacobson MP. PMID: 16375397.
      View in: PubMed   Mentions: 23     Fields:    
    138. Water's hydrogen bonds in the hydrophobic effect: a simple model. J Phys Chem B. 2005 Dec 15; 109(49):23611-7. Xu H, Dill KA. PMID: 16375338.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    139. 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. Coutsias EA, Seok C, Dill KA. PMID: 16175579.
      View in: PubMed   Mentions: 4     Fields:    
    140. Folding a nonbiological polymer into a compact multihelical structure. J Am Chem Soc. 2005 Aug 10; 127(31):10999-1009. Lee BC, Zuckermann RN, Dill KA. PMID: 16076207.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    141. 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. Merlo C, Dill KA, Weikl TR. PMID: 16009941.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    142. The flexibility in the proline ring couples to the protein backbone. Protein Sci. 2005 Apr; 14(4):1011-8. Ho BK, Coutsias EA, Seok C, Dill KA. PMID: 15772308.
      View in: PubMed   Mentions: 24     Fields:    Translation:Cells
    143. 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. Jaswal SS, Truhlar SM, Dill KA, Agard DA. PMID: 15740746.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    144. Modeling water, the hydrophobic effect, and ion solvation. Annu Rev Biophys Biomol Struct. 2005; 34:173-99. Dill KA, Truskett TM, Vlachy V, Hribar-Lee B. PMID: 15869376.
      View in: PubMed   Mentions: 68     Fields:    Translation:Cells
    145. Using quaternions to calculate RMSD. J Comput Chem. 2004 Nov 30; 25(15):1849-57. Coutsias EA, Seok C, Dill KA. PMID: 15376254.
      View in: PubMed   Mentions: 52     Fields:    
    146. A kinematic view of loop closure. J Comput Chem. 2004 Mar; 25(4):510-28. Coutsias EA, Seok C, Jacobson MP, Dill KA. PMID: 14735570.
      View in: PubMed   Mentions: 58     Fields:    
    147. Cooperativity in two-state protein folding kinetics. Protein Sci. 2004 Mar; 13(3):822-9. Weikl TR, Palassini M, Dill KA. PMID: 14978313.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    148. Incorporation of chemoselective functionalities into peptoids via solid-phase submonomer synthesis. Bioconjug Chem. 2004 Mar-Apr; 15(2):428-35. Horn T, Lee BC, Dill KA, Zuckermann RN. PMID: 15025542.
      View in: PubMed   Mentions: 10     Fields:    
    149. Structural and spectroscopic studies of peptoid oligomers with alpha-chiral aliphatic side chains. J Am Chem Soc. 2003 Nov 05; 125(44):13525-30. Wu CW, Kirshenbaum K, Sanborn TJ, Patch JA, Huang K, Dill KA, Zuckermann RN, Barron AE. PMID: 14583049.
      View in: PubMed   Mentions: 43     Fields:    Translation:Cells
    150. Fast protein folding kinetics. Proc Natl Acad Sci U S A. 2003 Oct 28; 100(22):12678-82. Schonbrun J, Dill KA. PMID: 14569019.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    151. Folding kinetics of two-state proteins: effect of circularization, permutation, and crosslinks. J Mol Biol. 2003 Sep 26; 332(4):953-63. Weikl TR, Dill KA. PMID: 12972264.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    152. A simple analytical model of water. Biophys Chem. 2003 Sep; 105(2-3):449-59. Truskett TM, Dill KA. PMID: 14499910.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    153. Folding rates and low-entropy-loss routes of two-state proteins. J Mol Biol. 2003 Jun 06; 329(3):585-98. Weikl TR, Dill KA. PMID: 12767836.
      View in: PubMed   Mentions: 26     Fields:    Translation:HumansAnimalsCells
    154. MOPED: method for optimizing physical energy parameters using decoys. J Comput Chem. 2003 Jan 15; 24(1):89-97. Seok C, Rosen JB, Chodera JD, Dill KA. PMID: 12483678.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    155. Computing the transition state populations in simple protein models. Biopolymers. 2003 Jan; 68(1):35-46. Ozkan SB, Dill KA, Bahar I. PMID: 12579578.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    156. 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. Song G, Thomas S, Dill KA, Scholtz JM, Amato NM. PMID: 12603032.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    157. 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. Amato NM, Dill KA, Song G. PMID: 12935327.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    158. Potential of mean force between two hydrophobic solutes in water. Biophys Chem. 2002 Dec 10; 101-102:295-307. Southall NT, Dill KA. PMID: 12488009.
      View in: PubMed   Mentions: 5     Fields:    
    159. How ions affect the structure of water. J Am Chem Soc. 2002 Oct 16; 124(41):12302-11. Hribar B, Southall NT, Vlachy V, Dill KA. PMID: 12371874.
      View in: PubMed   Mentions: 58     Fields:    Translation:Cells
    160. Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model. Protein Sci. 2002 Aug; 11(8):1958-70. Ozkan SB, Dill KA, Bahar I. PMID: 12142450.
      View in: PubMed   Mentions: 23     Fields:    Translation:Cells
    161. The elastic net algorithm and protein structure prediction. J Comput Chem. 2002 Jan 15; 23(1):77-83. Ball KD, Erman B, Dill KA. PMID: 11913391.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
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