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Items: 1 to 50 of 219

1.

Protein evolution speed depends on its stability and abundance and on chaperone concentrations.

Agozzino L, Dill KA.

Proc Natl Acad Sci U S A. 2018 Sep 11;115(37):9092-9097. doi: 10.1073/pnas.1810194115. Epub 2018 Aug 27.

2.

How Do Chaperones Protect a Cell's Proteins from Oxidative Damage?

Santra M, Dill KA, de Graff AMR.

Cell Syst. 2018 Jun 27;6(6):743-751.e3. doi: 10.1016/j.cels.2018.05.001. Epub 2018 Jun 6.

PMID:
29886110
3.

Autobiography of Ken A. Dill.

Dill KA.

J Phys Chem B. 2018 May 31;122(21):5263-5266. doi: 10.1021/acs.jpcb.8b02469. No abstract available.

PMID:
29847956
4.

Colleagues of Ken A. Dill.

Dill KA.

J Phys Chem B. 2018 May 31;122(21):5267-5268. doi: 10.1021/acs.jpcb.8b02468. No abstract available.

PMID:
29847955
5.

Selected Publications of Ken A. Dill.

Dill KA.

J Phys Chem B. 2018 May 31;122(21):5269-5277. doi: 10.1021/acs.jpcb.8b02467. No abstract available.

PMID:
29847954
6.

Analytical theory of the hydrophobic effect of solutes in water.

Urbic T, Dill KA.

Phys Rev E. 2017 Sep;96(3-1):032101. doi: 10.1103/PhysRevE.96.032101. Epub 2017 Sep 1.

7.

Caliber Corrected Markov Modeling (C2M2): Correcting Equilibrium Markov Models.

Dixit PD, Dill KA.

J Chem Theory Comput. 2018 Feb 13;14(2):1111-1119. doi: 10.1021/acs.jctc.7b01126. Epub 2018 Jan 26.

PMID:
29323898
8.

Perspective: Maximum caliber is a general variational principle for dynamical systems.

Dixit PD, Wagoner J, Weistuch C, Pressé S, Ghosh K, Dill KA.

J Chem Phys. 2018 Jan 7;148(1):010901. doi: 10.1063/1.5012990.

PMID:
29306272
9.

Accelerating physical simulations of proteins by leveraging external knowledge.

Perez A, Morrone JA, Dill KA.

Wiley Interdiscip Rev Comput Mol Sci. 2017 Sep-Oct;7(5). pii: e1309. doi: 10.1002/wcms.1309. Epub 2017 Apr 19.

10.

How Water's Properties Are Encoded in Its Molecular Structure and Energies.

Brini E, Fennell CJ, Fernandez-Serra M, Hribar-Lee B, Lukšič M, Dill KA.

Chem Rev. 2017 Oct 11;117(19):12385-12414. doi: 10.1021/acs.chemrev.7b00259. Epub 2017 Sep 26.

11.

Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers.

Guseva E, Zuckermann RN, Dill KA.

Proc Natl Acad Sci U S A. 2017 Sep 5;114(36):E7460-E7468. doi: 10.1073/pnas.1620179114. Epub 2017 Aug 22.

12.

Why Do Fast-Growing Bacteria Enter Overflow Metabolism? Testing the Membrane Real Estate Hypothesis.

Szenk M, Dill KA, de Graff AMR.

Cell Syst. 2017 Aug 23;5(2):95-104. doi: 10.1016/j.cels.2017.06.005. Epub 2017 Jul 26. Review.

13.

Bacterial proteostasis balances energy and chaperone utilization efficiently.

Santra M, Farrell DW, Dill KA.

Proc Natl Acad Sci U S A. 2017 Mar 28;114(13):E2654-E2661. doi: 10.1073/pnas.1620646114. Epub 2017 Mar 14.

14.

Computed Binding of Peptides to Proteins with MELD-Accelerated Molecular Dynamics.

Morrone JA, Perez A, MacCallum J, Dill KA.

J Chem Theory Comput. 2017 Feb 14;13(2):870-876. doi: 10.1021/acs.jctc.6b00977. Epub 2017 Jan 19.

PMID:
28042966
15.

Molecular Simulations Identify Binding Poses and Approximate Affinities of Stapled α-Helical Peptides to MDM2 and MDMX.

Morrone JA, Perez A, Deng Q, Ha SN, Holloway MK, Sawyer TK, Sherborne BS, Brown FK, Dill KA.

J Chem Theory Comput. 2017 Feb 14;13(2):863-869. doi: 10.1021/acs.jctc.6b00978. Epub 2017 Jan 19.

PMID:
28042965
16.

Blind protein structure prediction using accelerated free-energy simulations.

Perez A, Morrone JA, Brini E, MacCallum JL, Dill KA.

Sci Adv. 2016 Nov 11;2(11):e1601274. eCollection 2016 Nov.

17.

Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules.

Brini E, Paranahewage SS, Fennell CJ, Dill KA.

J Comput Aided Mol Des. 2016 Nov;30(11):1067-1077. doi: 10.1007/s10822-016-9961-9. Epub 2016 Sep 8.

18.

Role of Proteome Physical Chemistry in Cell Behavior.

Ghosh K, de Graff AM, Sawle L, Dill KA.

J Phys Chem B. 2016 Sep 15;120(36):9549-63. doi: 10.1021/acs.jpcb.6b04886. Epub 2016 Aug 24. Review.

19.

Molecular Motors: Power Strokes Outperform Brownian Ratchets.

Wagoner JA, Dill KA.

J Phys Chem B. 2016 Jul 7;120(26):6327-36. doi: 10.1021/acs.jpcb.6b02776. Epub 2016 May 17.

PMID:
27136319
20.

Modeling the Overproduction of Ribosomes when Antibacterial Drugs Act on Cells.

Maitra A, Dill KA.

Biophys J. 2016 Feb 2;110(3):743-748. doi: 10.1016/j.bpj.2015.12.016.

21.

Advances in free-energy-based simulations of protein folding and ligand binding.

Perez A, Morrone JA, Simmerling C, Dill KA.

Curr Opin Struct Biol. 2016 Feb;36:25-31. doi: 10.1016/j.sbi.2015.12.002. Epub 2016 Jan 7. Review.

22.

Highly Charged Proteins: The Achilles' Heel of Aging Proteomes.

de Graff AM, Hazoglou MJ, Dill KA.

Structure. 2016 Feb 2;24(2):329-36. doi: 10.1016/j.str.2015.11.006. Epub 2015 Dec 24.

23.

Constraint methods that accelerate free-energy simulations of biomolecules.

Perez A, MacCallum JL, Coutsias EA, Dill KA.

J Chem Phys. 2015 Dec 28;143(24):243143. doi: 10.1063/1.4936911. Review.

24.

Preface: Special Topic on Coarse Graining of Macromolecules, Biopolymers, and Membranes.

Holm C, Gompper G, Dill KA.

J Chem Phys. 2015 Dec 28;143(24):242901. doi: 10.1063/1.4938430.

PMID:
26723585
25.

Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations.

Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA.

J Chem Theory Comput. 2015 Mar 10;11(3):1347. doi: 10.1021/acs.jctc.5b00154. No abstract available.

26.

Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes.

Dixit PD, Jain A, Stock G, Dill KA.

J Chem Theory Comput. 2015 Nov 10;11(11):5464-72. doi: 10.1021/acs.jctc.5b00537. Epub 2015 Oct 2.

PMID:
26574334
27.

Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations.

Perez A, MacCallum JL, Brini E, Simmerling C, Dill KA.

J Chem Theory Comput. 2015 Oct 13;11(10):4770-9. doi: 10.1021/acs.jctc.5b00662. Epub 2015 Sep 17.

28.

Accelerating molecular simulations of proteins using Bayesian inference on weak information.

Perez A, MacCallum JL, Dill KA.

Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):11846-51. doi: 10.1073/pnas.1515561112. Epub 2015 Sep 8.

29.

Communication: Maximum caliber is a general variational principle for nonequilibrium statistical mechanics.

Hazoglou MJ, Walther V, Dixit PD, Dill KA.

J Chem Phys. 2015 Aug 7;143(5):051104. doi: 10.1063/1.4928193.

PMID:
26254635
30.

Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference.

MacCallum JL, Perez A, Dill KA.

Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):6985-90. doi: 10.1073/pnas.1506788112. Epub 2015 May 18.

31.

Protein aggregation in salt solutions.

Kastelic M, Kalyuzhnyi YV, Hribar-Lee B, Dill KA, Vlachy V.

Proc Natl Acad Sci U S A. 2015 May 26;112(21):6766-70. doi: 10.1073/pnas.1507303112. Epub 2015 May 11.

32.

Bacterial growth laws reflect the evolutionary importance of energy efficiency.

Maitra A, Dill KA.

Proc Natl Acad Sci U S A. 2015 Jan 13;112(2):406-11. doi: 10.1073/pnas.1421138111. Epub 2014 Dec 29.

33.

In silico selection of therapeutic antibodies for development: viscosity, clearance, and chemical stability.

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.

Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18601-6. doi: 10.1073/pnas.1421779112. Epub 2014 Dec 15. Erratum in: Proc Natl Acad Sci U S A. 2015 Dec 1;112(48):E6719.

34.
35.

TRIFORCE: Tessellated Semianalytical Solvent Exposed Surface Areas and Derivatives.

Drechsel NJ, Fennell CJ, Dill KA, Villà-Freixa J.

J Chem Theory Comput. 2014 Sep 9;10(9):4121-4132. Epub 2014 Jul 23.

36.

Modeling the solvation of nonpolar amino acids in guanidinium chloride solutions.

Cohen P, Dill KA, Jaswal SS.

J Phys Chem B. 2014 Sep 11;118(36):10618-23. doi: 10.1021/jp506379r. Epub 2014 Aug 28.

PMID:
25141127
37.

Inferring Microscopic Kinetic Rates from Stationary State Distributions.

Dixit PD, Dill KA.

J Chem Theory Comput. 2014 Aug 12;10(8):3002-3005. Epub 2014 Jun 2.

38.

General mechanism of two-state protein folding kinetics.

Rollins GC, Dill KA.

J Am Chem Soc. 2014 Aug 13;136(32):11420-7. doi: 10.1021/ja5049434. Epub 2014 Jul 30.

39.

Extracting representative structures from protein conformational ensembles.

Perez A, Roy A, Kasavajhala K, Wagaman A, Dill KA, MacCallum JL.

Proteins. 2014 Oct;82(10):2671-80. doi: 10.1002/prot.24633. Epub 2014 Jul 5.

PMID:
24975328
40.

Using interpolation for fast and accurate calculation of ion-ion interactions.

Lukšič M, Fennell CJ, Dill KA.

J Phys Chem B. 2014 Jul 17;118(28):8017-25. doi: 10.1021/jp501141j. Epub 2014 Mar 25.

41.

Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge.

Li L, Dill KA, Fennell CJ.

J Comput Aided Mol Des. 2014 Mar;28(3):259-64. doi: 10.1007/s10822-014-9712-8. Epub 2014 Jan 29.

PMID:
24474161
42.
43.

Computing the relative stabilities and the per-residue components in protein conformational changes.

Roy A, Perez A, Dill KA, Maccallum JL.

Structure. 2014 Jan 7;22(1):168-75. doi: 10.1016/j.str.2013.10.015. Epub 2013 Dec 5.

44.

Field-SEA: a model for computing the solvation free energies of nonpolar, polar, and charged solutes in water.

Li L, Fennell CJ, Dill KA.

J Phys Chem B. 2014 Jun 19;118(24):6431-7. doi: 10.1021/jp4115139. Epub 2013 Dec 13.

45.

A maximum entropy framework for nonexponential distributions.

Peterson J, Dixit PD, Dill KA.

Proc Natl Acad Sci U S A. 2013 Dec 17;110(51):20380-5. doi: 10.1073/pnas.1320578110. Epub 2013 Dec 2.

46.

Nonadditive entropies yield probability distributions with biases not warranted by the data.

Pressé S, Ghosh K, Lee J, Dill KA.

Phys Rev Lett. 2013 Nov 1;111(18):180604. Epub 2013 Nov 1.

PMID:
24237501
47.

A microscopic theory of solvation of monoions.

Urbič T, Fennell CJ, Dill KA.

Acta Chim Slov. 2012 Sep;59(3):554-8.

PMID:
24061310
48.

Calculating the sensitivity and robustness of binding free energy calculations to force field parameters.

Rocklin GJ, Mobley DL, Dill KA.

J Chem Theory Comput. 2013 Jul 9;9(7):3072-3083.

49.

Blind prediction of charged ligand binding affinities in a model binding site.

Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA.

J Mol Biol. 2013 Nov 15;425(22):4569-83. doi: 10.1016/j.jmb.2013.07.030. Epub 2013 Jul 26.

50.

Biophysics. Introduction.

Dill KA.

Annu Rev Biophys. 2013;42. doi: 10.1146/annurev-bb-42-050113-100001. No abstract available.

PMID:
23798065

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