Kenneth Dill, PhD

Title(s)Professor Emeritus, Pharmaceutical Chemistry
SchoolSchool of Pharmacy
AddressLocation Required, #001
Phone415-476-9964
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    Collapse Overview 

    Collapse Research 
    Collapse Research Activities and Funding
    Solvation modeling for next-gen biomolecule simulations
    NIH RM1GM135136Jun 1, 2020 - May 31, 2025
    Role: Principal Investigator
    MELD: accelerating MD modeling of proteins using Bayesian inference
    NIH R01GM125813Jan 1, 2018 - Dec 31, 2021
    Role: Principal Investigator
    Modeling Aqueous Solvation in Biology
    NIH R01GM063592Sep 1, 2001 - Mar 31, 2019
    Role: Principal Investigator
    Modeling Aqueous Solvation in Biology
    NIH R56GM063592Sep 1, 2001 - Aug 31, 2010
    Role: Principal Investigator
    PROTEIN STABILITY THEORY
    NIH R01GM046628Aug 1, 1991 - Jul 31, 1995
    Role: Principal Investigator
    HEAD GROUP INTERACTIONS IN MEMBRANES AND MICELLES
    NIH R01GM040692Jul 1, 1988 - Jun 30, 1992
    Role: Principal Investigator
    Combinatorial Statistical Mechanics of Protein Folding
    NIH R01GM034993Sep 12, 1985 - Jun 30, 2012
    Role: Principal Investigator
    STATISTICAL MECHANICS OF AMPHIPHILIC AGGREGATES
    NIH R01GM032430Jul 1, 1983 - Dec 31, 1986
    Role: Principal Investigator

    Collapse ORNG Applications 
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    Collapse Bibliographic 
    Collapse Publications
    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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    1. Origins of Life: The Protein Folding Problem all over again? Proc Natl Acad Sci U S A. 2024 Aug 20; 121(34):e2315000121. Kocher CD, Dill KA. PMID: 39133848; PMCID: PMC11348307.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    2. The prebiotic emergence of biological evolution. R Soc Open Sci. 2024 Jul; 11(7):240431. Kocher CD, Dill KA. PMID: 39050718; PMCID: PMC11265915.
      View in: PubMed   Mentions:
    3. Transcriptional drift in aging cells: A global decontroller. Proc Natl Acad Sci U S A. 2024 Jul 23; 121(30):e2401830121. Matsuzaki T, Weistuch C, de Graff A, Dill KA, Balázsi G. PMID: 39012826; PMCID: PMC11287169.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    4. MHC-Fine: Fine-tuned AlphaFold for precise MHC-peptide complex prediction. Biophys J. 2024 Sep 03; 123(17):2902-2909. Glukhov E, Kalitin D, Stepanenko D, Zhu Y, Nguyen T, Jones G, Patsahan T, Simmerling C, Mitchell JC, Vajda S, Dill KA, Padhorny D, Kozakov D. PMID: 38751115; PMCID: PMC11393670.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    5. Brain signaling becomes less integrated and more segregated with age. bioRxiv. 2024 May 02. Razban RM, Antal BB, Dill KA, Mujica-Parodi LR. PMID: 38014139; PMCID: PMC10680817.
      View in: PubMed   Mentions:
    6. Antibody association in solution: cluster distributions and mechanisms. MAbs. 2024 Jan-Dec; 16(1):2339582. Brudar S, Breydo L, Chung E, Dill KA, Ehterami N, Phadnis K, Senapati S, Shameem M, Tang X, Tayyab M, Hribar-Lee B. PMID: 38666507; PMCID: PMC11057677.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    7. Functional transcriptional signatures for tumor-type-agnostic phenotype prediction. bioRxiv. 2024 Mar 12. Weistuch C, Murgas KA, Zhu J, Norton L, Dill KA, Tannenbaum AR, Deasy JO. PMID: 37090606; PMCID: PMC10120658.
      View in: PubMed   Mentions:
    8. Computational Procedure for Predicting Excipient Effects on Protein-Protein Affinities. J Chem Theory Comput. 2024 Feb 13; 20(3):1479-1488. Dignon GL, Dill KA. PMID: 38294777; PMCID: PMC10868583.
      View in: PubMed   Mentions:    Fields:    
    9. A computational procedure for predicting excipient effects on protein-protein affinities. bioRxiv. 2023 Dec 23. Dignon GL, Dill KA. PMID: 38187552; PMCID: PMC10769426.
      View in: PubMed   Mentions:
    10. MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction. bioRxiv. 2023 Dec 14. Glukhov E, Kalitin D, Stepanenko D, Zhu Y, Nguyen T, Jones G, Simmerling C, Mitchell JC, Vajda S, Dill KA, Padhorny D, Kozakov D. PMID: 38077000; PMCID: PMC10705405.
      View in: PubMed   Mentions:
    11. Protein Association in Solution: Statistical Mechanical Modeling. Biomolecules. 2023 11 24; 13(12). Vlachy V, Kalyuzhnyi YV, Hribar-Lee B, Dill KA. PMID: 38136574; PMCID: PMC10742237.
      View in: PubMed   Mentions:    Fields:    
    12. Transcriptional drift in aging cells: A global de-controller. bioRxiv. 2023 Nov 21. Matsuzaki T, Weistuch C, de Graff A, Dill KA, Balázsi G. PMID: 38045342; PMCID: PMC10690170.
      View in: PubMed   Mentions:
    13. Computing Free Energies of Fold-Switching Proteins Using MELD x MD. J Chem Theory Comput. 2023 Oct 10; 19(19):6839-6847. Parui S, Brini E, Dill KA. PMID: 37725050.
      View in: PubMed   Mentions:    Fields:    
    14. Simple Model of Liquid Water Dynamics. J Phys Chem B. 2023 Sep 21; 127(37):7996-8001. Urbic T, Dill KA. PMID: 37672327; PMCID: PMC10518820.
      View in: PubMed   Mentions:    Fields:    
    15. Next-Gen Biophysics: Look to the Forest, Beyond the Trees. Annu Rev Biophys. 2023 05 09; 52:v-viii. Schmit J, Dill KA. PMID: 37159295.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    16. MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands. J Chem Inf Model. 2023 05 08; 63(9):2857-2865. Parui S, Robertson JC, Somani S, Tresadern G, Liu C, Dill KA. PMID: 37093848.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    17. Early path dominance as a principle for neurodevelopment. Proc Natl Acad Sci U S A. 2023 04 18; 120(16):e2218007120. Razban RM, Pachter JA, Dill KA, Mujica-Parodi LR. PMID: 37053187; PMCID: PMC10120000.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    18. Origins of life: first came evolutionary dynamics. QRB Discov. 2023; 4:e4. Kocher C, Dill KA. PMID: 37529034; PMCID: PMC10392681.
      View in: PubMed   Mentions: 2  
    19. Darwinian evolution as a dynamical principle. Proc Natl Acad Sci U S A. 2023 Mar 14; 120(11):e2218390120. Kocher CD, Dill KA. PMID: 36881627; PMCID: PMC10089213.
      View in: PubMed   Mentions: 5     Fields:    
    20. Nonequilibrium statistical physics beyond the ideal heat bath approximation. Phys Rev E. 2023 Jan; 107(1-1):014131. Pachter JA, Dill KA. PMID: 36797947.
      View in: PubMed   Mentions:    Fields:    
    21. BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions. Int J Mol Sci. 2022 Dec 06; 23(23). Nikolic M, Brudar S, Coutsias E, Dill KA, Lukšic M, Simmerling C, Hribar-Lee B. PMID: 36499696; PMCID: PMC9741033.
      View in: PubMed   Mentions: 1     Fields:    
    22. Review of the application of Kirchhoff's Laws of series and parallel flows to pharmacology: Defining organ clearance. Pharmacol Ther. 2022 Nov; 239:108278. Pachter JA, Dill KA, Sodhi JK, Benet LZ. PMID: 36075300; PMCID: PMC10832328.
      View in: PubMed   Mentions: 3     Fields:    
    23. Crustwater: Modeling Hydrophobic Solvation. J Phys Chem B. 2022 08 18; 126(32):6052-6062. Yadav AK, Bandyopadhyay P, Coutsias EA, Dill KA. PMID: 35926838; PMCID: PMC9393863.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    24. The Bootstrap Model of Prebiotic Networks of Proteins and Nucleic Acids. Life (Basel). 2022 May 12; 12(5). Farquharson T, Agozzino L, Dill K. PMID: 35629391; PMCID: PMC9144896.
      View in: PubMed   Mentions: 1  
    25. Accelerating Protein Folding Molecular Dynamics Using Inter-Residue Distances from Machine Learning Servers. J Chem Theory Comput. 2022 Mar 08; 18(3):1929-1935. Nassar R, Brini E, Parui S, Liu C, Dignon GL, Dill KA. PMID: 35133832; PMCID: PMC9281603.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    26. Accelerating Molecular Dynamics Enrichments of High-Affinity Ligands for Proteins. J Chem Theory Comput. 2022 Jan 11; 18(1):374-379. Liu C, Brini E, Dill KA. PMID: 34877865.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    27. Metabolism modulates network synchrony in the aging brain. Proc Natl Acad Sci U S A. 2021 10 05; 118(40). Weistuch C, Mujica-Parodi LR, Razban RM, Antal B, van Nieuwenhuizen H, Amgalan A, Dill KA. PMID: 34588302; PMCID: PMC8501850.
      View in: PubMed   Mentions: 11     Fields:    Translation:Humans
    28. CryoFold: determining protein structures and data-guided ensembles from cryo-EM density maps. Matter. 2021 Oct 06; 4(10):3195-3216. Shekhar M, Terashi G, Gupta C, Sarkar D, Debussche G, Sisco NJ, Nguyen J, Mondal A, Vant J, Fromme P, Van Horn WD, Tajkhorshid E, Kihara D, Dill K, Perez A, Singharoy A. PMID: 35874311; PMCID: PMC9302471.
      View in: PubMed   Mentions: 15  
    29. MELD-accelerated molecular dynamics help determine amyloid fibril structures. Commun Biol. 2021 08 05; 4(1):942. Sharma B, Dill KA. PMID: 34354239; PMCID: PMC8342454.
      View in: PubMed   Mentions: Translation:Cells
    30. Nanoscale Catalyst Chemotaxis Can Drive the Assembly of Functional Pathways. J Phys Chem B. 2021 08 12; 125(31):8781-8786. Kocher C, Agozzino L, Dill K. PMID: 34324352; PMCID: PMC8366527.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    31. The Protein Folding Problem: The Role of Theory. J Mol Biol. 2021 10 01; 433(20):167126. Nassar R, Dignon GL, Razban RM, Dill KA. PMID: 34224747; PMCID: PMC8547331.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    32. Evolution of mechanical cooperativity among myosin II motors. Proc Natl Acad Sci U S A. 2021 05 18; 118(20). Wagoner JA, Dill KA. PMID: 33975956; PMCID: PMC8157946.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    33. The Refractory Period Matters: Unifying Mechanisms of Macroscopic Brain Waves. Neural Comput. 2021 04 13; 33(5):1145-1163. Weistuch C, Mujica-Parodi LR, Dill K. PMID: 33617741.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    34. Analytical 2-Dimensional Model of Nonpolar and Ionic Solvation in Water. J Phys Chem B. 2021 02 25; 125(7):1861-1873. Yadav AK, Bandyopadhyay P, Urbic T, Dill KA. PMID: 33539097; PMCID: PMC7958497.
      View in: PubMed   Mentions: 1     Fields:    
    35. Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nat Methods. 2021 02; 18(2):156-164. Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, Fraser JS, Herzik MA, Hoh SW, Hou J, Hung LW, Igaev M, Joseph AP, Kihara D, Kumar D, Mittal S, Monastyrskyy B, Olek M, Palmer CM, Patwardhan A, Perez A, Pfab J, Pintilie GD, Richardson JS, Rosenthal PB, Sarkar D, Schäfer LU, Schmid MF, Schröder GF, Shekhar M, Si D, Singharoy A, Terashi G, Terwilliger TC, Vaiana A, Wang L, Wang Z, Wankowicz SA, Williams CJ, Winn M, Wu T, Yu X, Zhang K, Berman HM, Chiu W. PMID: 33542514; PMCID: PMC7864804.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    36. Proteostasis is adaptive: Balancing chaperone holdases against foldases. PLoS Comput Biol. 2020 12; 16(12):e1008460. de Graff AM, Mosedale DE, Sharp T, Dill KA, Grainger DJ. PMID: 33315891; PMCID: PMC7769611.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    37. Inferring a network from dynamical signals at its nodes. PLoS Comput Biol. 2020 11; 16(11):e1008435. Weistuch C, Agozzino L, Mujica-Parodi LR, Dill KA. PMID: 33253160; PMCID: PMC7728228.
      View in: PubMed   Mentions: 3     Fields:    Translation:Cells
    38. Protein storytelling through physics. Science. 2020 11 27; 370(6520). Brini E, Simmerling C, Dill K. PMID: 33243857; PMCID: PMC7945008.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansCells
    39. Computing Ligands Bound to Proteins Using MELD-Accelerated MD. J Chem Theory Comput. 2020 Oct 13; 16(10):6377-6382. Liu C, Brini E, Perez A, Dill KA. PMID: 32910647; PMCID: PMC7572789.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    40. How Do Cells Adapt? Stories Told in Landscapes. Annu Rev Chem Biomol Eng. 2020 06 07; 11:155-182. Agozzino L, Balázsi G, Wang J, Dill KA. PMID: 32513086; PMCID: PMC7291840.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansAnimalsCells
    41. 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; PMCID: PMC7874234.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    42. 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; PMCID: PMC7084077.
      View in: PubMed   Mentions: 60     Fields:    Translation:Humans
    43. The Maximum Caliber Variational Principle for Nonequilibria. Annu Rev Phys Chem. 2020 04 20; 71:213-238. Ghosh K, Dixit PD, Agozzino L, Dill KA. PMID: 32075515; PMCID: PMC9827727.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    44. 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; PMCID: PMC7539656.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansAnimalsCells
    45. 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; PMCID: PMC7553231.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    46. 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; PMCID: PMC6878954.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    47. 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; PMCID: PMC6825304.
      View in: PubMed   Mentions: 62     Fields:    Translation:AnimalsCells
    48. 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; PMCID: PMC6851473.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    49. 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.
      View in: PubMed   Mentions: 1     Fields:    
    50. 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; PMCID: PMC6690486.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    51. 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; PMCID: PMC6442566.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    52. Building Markov state models using optimal transport theory. J Chem Phys. 2019 Feb 07; 150(5):054105. Dixit PD, Dill KA. PMID: 30736685.
      View in: PubMed   Mentions: 2     Fields:    
    53. Water Is a Cagey Liquid. J Am Chem Soc. 2018 12 12; 140(49):17106-17113. Urbic T, Dill KA. PMID: 30461279; PMCID: PMC6705392.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    54. 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; PMCID: PMC6705390.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    55. 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; PMCID: PMC6816043.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    56. 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; PMCID: PMC7001678.
      View in: PubMed   Mentions: 3     Fields:    
    57. 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; PMCID: PMC6140491.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
    58. 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: 18     Fields:    Translation:Cells
    59. Selected Publications of Ken A. Dill. J Phys Chem B. 2018 05 31; 122(21):5269-5277. Dill KA. PMID: 29847954.
      View in: PubMed   Mentions:    Fields:    
    60. Autobiography of Ken A. Dill. J Phys Chem B. 2018 05 31; 122(21):5263-5266. Dill KA. PMID: 29847956.
      View in: PubMed   Mentions:    Fields:    
    61. Colleagues of Ken A. Dill. J Phys Chem B. 2018 05 31; 122(21):5267-5268. Dill KA. PMID: 29847955.
      View in: PubMed   Mentions:    Fields:    
    62. 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; PMCID: PMC8570072.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    63. 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: 7     Fields:    Translation:Cells
    64. 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: 19     Fields:    
    65. 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; PMCID: PMC6425977.
      View in: PubMed   Mentions: 16  
    66. 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; PMCID: PMC5639468.
      View in: PubMed   Mentions: 65     Fields:    
    67. 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; PMCID: PMC5884126.
      View in: PubMed   Mentions: 5     Fields:    
    68. 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; PMCID: PMC5594640.
      View in: PubMed   Mentions: 21     Fields:    Translation:Cells
    69. 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: 83     Fields:    Translation:Cells
    70. 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; PMCID: PMC5612641.
      View in: PubMed   Mentions: 8  
    71. 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; PMCID: PMC5380058.
      View in: PubMed   Mentions: 31     Fields:    Translation:Cells
    72. Molecular Simulations Identify Binding Poses and Approximate Affinities of Stapled α-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: 24     Fields:    Translation:Cells
    73. 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: 33     Fields:    Translation:Cells
    74. 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; PMCID: PMC5106196.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    75. 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; PMCID: PMC5261860.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    76. 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; PMCID: PMC5034766.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    77. 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: 20     Fields:    
    78. 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; PMCID: PMC4744161.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    79. 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; PMCID: PMC4785060.
      View in: PubMed   Mentions: 56     Fields:    Translation:HumansCells
    80. 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; PMCID: PMC4684272.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    81. 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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    82. 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: 27     Fields:    Translation:HumansAnimalsCells
    83. 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: 20     Fields:    Translation:Cells
    84. 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; PMCID: PMC4813323.
      View in: PubMed   Mentions: 30     Fields:    Translation:Cells
    85. 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; PMCID: PMC4586851.
      View in: PubMed   Mentions: 42     Fields:    Translation:Cells
    86. 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: 6     Fields:    
    87. 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; PMCID: PMC4460504.
      View in: PubMed   Mentions: 71     Fields:    Translation:Cells
    88. 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; PMCID: PMC4450416.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    89. 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; PMCID: PMC4675652.
      View in: PubMed   Mentions: 6     Fields:    
    90. 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; PMCID: PMC4299221.
      View in: PubMed   Mentions: 72     Fields:    Translation:Cells
    91. 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; PMCID: PMC4284567.
      View in: PubMed   Mentions: 113     Fields:    Translation:HumansAnimalsCells
    92. 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; PMCID: PMC4241710.
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    93. 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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    94. 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; PMCID: PMC5104671.
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    95. 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; PMCID: PMC4159216.
      View in: PubMed   Mentions: 3     Fields:    
    96. 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: 2     Fields:    Translation:HumansAnimalsCells
    97. 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; PMCID: PMC4064692.
      View in: PubMed   Mentions: 15     Fields:    Translation:Cells
    98. 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; PMCID: PMC4132853.
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    99. 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; PMCID: PMC4142335.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    100. 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.
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    101. 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; PMCID: PMC4065164.
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    102. 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; PMCID: PMC3905753.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    103. 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; PMCID: PMC3870711.
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    104. 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; PMCID: PMC3838431.
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    105. 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.
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    106. 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; PMCID: PMC3962782.
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    107. 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; PMCID: PMC3763860.
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    108. 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; PMCID: PMC3598757.
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    109. 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; PMCID: PMC3893241.
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    110. 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; PMCID: PMC3569860.
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    111. Biophysics. Introduction. Annu Rev Biophys. 2013; 42. Dill KA. PMID: 23798065.
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    112. The protein-folding problem, 50 years on. Science. 2012 Nov 23; 338(6110):1042-6. Dill KA, MacCallum JL. PMID: 23180855.
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    113. 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; PMCID: PMC4269272.
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    114. 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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    115. 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; PMCID: PMC3437879.
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    116. 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; PMCID: PMC3387198.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimals
    117. 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; PMCID: PMC5234790.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    118. 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; PMCID: PMC3729351.
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    119. Growth rates of protein crystals. J Am Chem Soc. 2012 Mar 07; 134(9):3934-7. Schmit JD, Dill K. PMID: 22339624; PMCID: PMC3311159.
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    120. 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; PMCID: PMC3292588.
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    121. 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
    122. 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; PMCID: PMC3207669.
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    123. Physical Modeling of Aqueous Solvation. J Stat Phys. 2011 Oct 01; 145(2):209-226. Fennell CJ, Dill KA. PMID: 25143658; PMCID: PMC4136392.
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    124. 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; PMCID: PMC3238793.
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    125. 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; PMCID: PMC3182083.
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    126. 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; PMCID: PMC3044389.
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    127. 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; PMCID: PMC3021675.
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    128. 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.
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    129. Cellular proteomes have broad distributions of protein stability. Biophys J. 2010 Dec 15; 99(12):3996-4002. Ghosh K, Dill K. PMID: 21156142; PMCID: PMC3000515.
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    130. 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; PMCID: PMC3004097.
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    131. 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; PMCID: PMC2941273.
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    132. 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; PMCID: PMC2902533.
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    133. 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; PMCID: PMC4142491.
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    134. The stabilities of protein crystals. J Phys Chem B. 2010 Mar 25; 114(11):4020-7. Schmit JD, Dill KA. PMID: 20199035; PMCID: PMC2919244.
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    135. 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; PMCID: PMC2810857.
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    136. 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; PMCID: PMC2792327.
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    137. 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; PMCID: PMC2788029.
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    138. 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; PMCID: PMC3273425.
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    139. 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; PMCID: PMC2705543.
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    140. 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; PMCID: PMC2698044.
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    141. 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; PMCID: PMC2756098.
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    142. 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; PMCID: PMC2684682.
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    143. Modeling Hofmeister Effects. Acta Chim Slov. 2009 Mar 11; 56(1):196-202. Hribar-Lee B, Vlachy V, Dill KA. PMID: 20161468; PMCID: PMC2792915.
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    144. 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; PMCID: PMC2701304.
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    145. 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; PMCID: PMC2629132.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    146. 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; PMCID: PMC2716649.
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    147. 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; PMCID: PMC2801025.
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    148. 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; PMCID: PMC2639212.
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    149. 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; PMCID: PMC2629734.
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    150. 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; PMCID: PMC2748234.
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    151. 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; PMCID: PMC2671656.
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    152. 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; PMCID: PMC2699260.
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    153. 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; PMCID: PMC2745216.
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    154. 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; PMCID: PMC2864544.
      View in: PubMed   Mentions: 2     Fields:    
    155. 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; PMCID: PMC2745223.
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    156. The protein folding problem. Annu Rev Biophys. 2008; 37:289-316. Dill KA, Ozkan SB, Shell MS, Weikl TR. PMID: 18573083; PMCID: PMC2443096.
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    157. 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.
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    158. 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; PMCID: PMC1924571.
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    159. 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.
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    160. 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; PMCID: PMC2104542.
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    161. 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; PMCID: PMC1891208.
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    162. 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.
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    163. 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.
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    164. 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
    165. 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; PMCID: PMC3261839.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    166. 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: 93     Fields:    Translation:Cells
    167. 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; PMCID: PMC2562444.
      View in: PubMed   Mentions: 84     Fields:    
    168. 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: 9     Fields:    Translation:Cells
    169. 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: 150     Fields:    
    170. 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
    171. 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; PMCID: PMC3583553.
      View in: PubMed   Mentions: 117     Fields:    Translation:Cells
    172. Folding very short peptides using molecular dynamics. PLoS Comput Biol. 2006 Apr; 2(4):e27. Ho BK, Dill KA. PMID: 16617376; PMCID: PMC1435986.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    173. 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; PMCID: PMC3622476.
      View in: PubMed   Mentions: 16  
    174. 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
    175. 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: 24     Fields:    
    176. 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: 9     Fields:    Translation:Cells
    177. 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:    
    178. 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: 33     Fields:    Translation:Cells
    179. 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; PMCID: PMC1177393.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    180. 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; PMCID: PMC2253451.
      View in: PubMed   Mentions: 31     Fields:    Translation:Cells
    181. 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: 9     Fields:    Translation:Cells
    182. 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: 95     Fields:    Translation:Cells
    183. 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: 81     Fields:    
    184. 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: 11     Fields:    
    185. Cooperativity in two-state protein folding kinetics. Protein Sci. 2004 Mar; 13(3):822-9. Weikl TR, Palassini M, Dill KA. PMID: 14978313; PMCID: PMC2286727.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    186. 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: 98     Fields:    
    187. 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: 58     Fields:    Translation:Cells
    188. Fast protein folding kinetics. Proc Natl Acad Sci U S A. 2003 Oct 28; 100(22):12678-82. Schonbrun J, Dill KA. PMID: 14569019; PMCID: PMC240677.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    189. 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: 13     Fields:    Translation:Cells
    190. 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
    191. 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: 27     Fields:    Translation:HumansAnimalsCells
    192. 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: 7     Fields:    Translation:Cells
    193. 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
    194. 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: 13     Fields:    Translation:Cells
    195. 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: 11     Fields:    Translation:Cells
    196. 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:    
    197. 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; PMCID: PMC1513647.
      View in: PubMed   Mentions: 98     Fields:    Translation:Cells
    198. 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; PMCID: PMC2373683.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    199. 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: 3     Fields:    Translation:Cells
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