Ken A. Dill - Publications

Affiliations: 
Physics and Chemistry Stony Brook University, Stony Brook, NY, United States 
Area:
protein folding and stability
Website:
http://dillgroup.stonybrook.edu/people

245 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 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, et al. Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nature Methods. PMID 33542514 DOI: 10.1038/s41592-020-01051-w  0.44
2020 Liu C, Brini E, Perez A, Dill KA. Computing ligands bound to proteins using MELD-accelerated MD. Journal of Chemical Theory and Computation. PMID 32910647 DOI: 10.1021/Acs.Jctc.0C00543  0.56
2020 Padhorny D, Porter KA, Ignatov M, Alekseenko A, Beglov D, Kotelnikov S, Ashizawa R, Desta I, Alam N, Sun Z, Brini E, Dill K, Furman OS, Vajda S, Kozakov D. ClusPro in rounds 38-45 of CAPRI: Toward combining template-based methods with free docking. Proteins. PMID 32142178 DOI: 10.1002/Prot.25887  0.56
2020 Ghosh K, Dixit PD, Agozzino L, Dill KA. The Maximum Caliber Variational Principle for Nonequilibria. Annual Review of Physical Chemistry. PMID 32075515 DOI: 10.1146/Annurev-Physchem-071119-040206  0.48
2019 Khramushin A, Marcu O, Alam N, Shimony O, Padhorny D, Brini E, Dill K, Vajda S, Kozakov D, Schueler-Furman O. Modeling beta sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI Rounds 38-45. Proteins. PMID 31891416 DOI: 10.1002/Prot.25871  0.56
2019 Kotelnikov S, Alekseenko A, Liu C, Ignatov M, Padhorny D, Brini E, Lukin M, Coutsias E, Dill KA, Kozakov D. Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4. Journal of Computer-Aided Molecular Design. PMID 31879831 DOI: 10.1007/S10822-019-00257-1  0.56
2019 Santra M, Dill KA, de Graff AMR. Proteostasis collapse is a driver of cell aging and death. Proceedings of the National Academy of Sciences of the United States of America. PMID 31619571 DOI: 10.1073/Pnas.1906592116  0.68
2019 Wagoner JA, Dill KA. Opposing pressures of speed and efficiency guide the evolution of molecular machines. Molecular Biology and Evolution. PMID 31432071 DOI: 10.1093/Molbev/Msz190  0.52
2019 Robertson JC, Nassar R, Liu C, Brini E, Dill KA, Perez A. NMR-assisted protein structure prediction with MELDxMD. Proteins. PMID 31350773 DOI: 10.1002/Prot.25788  0.56
2019 Brini E, Kozakov D, Dill KA. Predicting protein dimer structures using MELD x MD. Journal of Chemical Theory and Computation. PMID 30908034 DOI: 10.1021/Acs.Jctc.8B01208  0.56
2019 Wagoner JA, Dill KA. Mechanisms for achieving high speed and efficiency in biomolecular machines. Proceedings of the National Academy of Sciences of the United States of America. PMID 30850521 DOI: 10.1073/Pnas.1812149116  0.52
2018 Kastelic M, Dill KA, Kalyuzhnyi YV, Vlachy V. Controlling the viscosities of antibody solutions through control of their binding sites. Journal of Molecular Liquids. 270: 234-242. PMID 30906093 DOI: 10.1016/J.Molliq.2017.11.106  0.56
2018 Ignatov M, Liu C, Alekseenko A, Sun Z, Padhorny D, Kotelnikov S, Kazennov A, Grebenkin I, Kholodov Y, Kolosvari I, Perez A, Dill K, Kozakov D. Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge. Journal of Computer-Aided Molecular Design. PMID 30421350 DOI: 10.1007/S10822-018-0176-0  0.56
2018 Robertson JC, Perez A, Dill KA. MELD x MD Folds Nonthreadables, Giving Native Structures and Populations. Journal of Chemical Theory and Computation. PMID 30407805 DOI: 10.1021/Acs.Jctc.8B00886  0.44
2018 Santra M, Dill KA, de Graff AMR. How Do Chaperones Protect a Cell's Proteins from Oxidative Damage? Cell Systems. PMID 29886110 DOI: 10.1016/J.Cels.2018.05.001  0.68
2018 Perez A, Sittel F, Stock G, Dill KA. MELD-path efficiently computes conformational transitions, including multiple and diverse paths. Journal of Chemical Theory and Computation. PMID 29547695 DOI: 10.1021/Acs.Jctc.7B01294  0.44
2018 Dixit PD, Wagoner J, Weistuch C, Pressé S, Ghosh K, Dill KA. Perspective: Maximum caliber is a general variational principle for dynamical systems. The Journal of Chemical Physics. 148: 010901. PMID 29306272 DOI: 10.1063/1.5012990  0.56
2017 Perez A, Morrone JA, Dill KA. Accelerating physical simulations of proteins by leveraging external knowledge. Wiley Interdisciplinary Reviews. Computational Molecular Science. 7. PMID 28959358 DOI: 10.1002/Wcms.1309  0.44
2017 Brini E, Fennell CJ, Fernandez-Serra M, Hribar-Lee B, Lukšič M, Dill KA. How Water's Properties Are Encoded in Its Molecular Structure and Energies. Chemical Reviews. PMID 28949513 DOI: 10.1021/Acs.Chemrev.7B00259  0.6
2017 Guseva E, Zuckermann RN, Dill KA. Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers. Proceedings of the National Academy of Sciences of the United States of America. PMID 28831002 DOI: 10.1073/Pnas.1620179114  0.88
2017 Szenk M, Dill KA, de Graff AMR. Why Do Fast-Growing Bacteria Enter Overflow Metabolism? Testing the Membrane Real Estate Hypothesis. Cell Systems. PMID 28755958 DOI: 10.1016/J.Cels.2017.06.005  0.68
2017 Santra M, Farrell DW, Dill KA. Bacterial proteostasis balances energy and chaperone utilization efficiently. Proceedings of the National Academy of Sciences of the United States of America. PMID 28292901 DOI: 10.1073/Pnas.1620646114  0.68
2017 Morrone JA, Perez A, MacCallum JL, Dill KA. Computed binding of peptides to proteins with MELD-accelerated molecular dynamics. Journal of Chemical Theory and Computation. PMID 28042966 DOI: 10.1021/Acs.Jctc.6B00977  0.44
2017 Morrone JA, Perez A, Deng Q, Ha SN, Holloway MK, Sawyer TK, Sherborne BS, Brown FK, Dill KA. Molecular Simulations Identify Binding Poses and Approximate Affinities of Stapled α-Helical Peptides to MDM2 and MDMX. Journal of Chemical Theory and Computation. PMID 28042965 DOI: 10.1021/Acs.Jctc.6B00978  0.44
2016 Perez A, Morrone JA, Brini E, MacCallum JL, Dill KA. Blind protein structure prediction using accelerated free-energy simulations. Science Advances. 2: e1601274. PMID 27847872 DOI: 10.1126/Sciadv.1601274  0.56
2016 Brini E, Paranahewage SS, Fennell CJ, Dill KA. Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules. Journal of Computer-Aided Molecular Design. PMID 27632227 DOI: 10.1007/S10822-016-9961-9  0.6
2016 Ghosh K, de Graff AM, Sawle L, Dill KA. The Role of Proteome Physical Chemistry in Cell Behavior. The Journal of Physical Chemistry. B. PMID 27513457 DOI: 10.1021/Acs.Jpcb.6B04886  0.48
2016 Wagoner JA, Dill KA. Molecular Motors: Power Strokes Outperform Brownian Ratchets. The Journal of Physical Chemistry. B. PMID 27136319 DOI: 10.1021/Acs.Jpcb.6B02776  0.52
2016 Perez A, Morrone JA, Simmerling C, Dill KA. Advances in free-energy-based simulations of protein folding and ligand binding. Current Opinion in Structural Biology. 36: 25-31. PMID 26773233 DOI: 10.1016/J.Sbi.2015.12.002  1
2015 de Graff AM, Hazoglou MJ, Dill KA. Highly Charged Proteins: The Achilles' Heel of Aging Proteomes. Structure (London, England : 1993). PMID 26724998 DOI: 10.1016/J.Str.2015.11.006  1
2015 Perez A, MacCallum JL, Coutsias EA, Dill KA. Constraint methods that accelerate free-energy simulations of biomolecules. The Journal of Chemical Physics. 143: 243143. PMID 26723628 DOI: 10.1063/1.4936911  1
2015 Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations. Journal of Chemical Theory and Computation. 11: 1347. PMID 26579779 DOI: 10.1021/Acs.Jctc.5B00154  1
2015 Dixit PD, Jain A, Stock G, Dill KA. Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes. Journal of Chemical Theory and Computation. 11: 5464-72. PMID 26574334 DOI: 10.1021/Acs.Jctc.5B00537  1
2015 Perez A, MacCallum JL, Brini E, Simmerling C, Dill KA. Grid-Based Backbone Correction to the ff12SB Protein Force Field for Implicit-Solvent Simulations. Journal of Chemical Theory and Computation. 11: 4770-9. PMID 26574266 DOI: 10.1021/Acs.Jctc.5B00662  1
2015 Perez A, MacCallum JL, Dill KA. Accelerating molecular simulations of proteins using Bayesian inference on weak information. Proceedings of the National Academy of Sciences of the United States of America. 112: 11846-51. PMID 26351667 DOI: 10.1073/Pnas.1515561112  1
2015 Hazoglou MJ, Walther V, Dixit PD, Dill KA. Communication: Maximum caliber is a general variational principle for nonequilibrium statistical mechanics. The Journal of Chemical Physics. 143: 051104. PMID 26254635 DOI: 10.1063/1.4928193  1
2015 Remsing RC, Xi E, Vembanur S, Sharma S, Debenedetti PG, Garde S, Patel AJ. Pathways to dewetting in hydrophobic confinement. Proceedings of the National Academy of Sciences of the United States of America. PMID 26100866 DOI: 10.1073/Pnas.1503302112  1
2015 MacCallum JL, Perez A, Dill KA. Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference. Proceedings of the National Academy of Sciences of the United States of America. 112: 6985-90. PMID 26038552 DOI: 10.1073/Pnas.1506788112  1
2015 Kastelic M, Kalyuzhnyi YV, Hribar-Lee B, Dill KA, Vlachy V. Protein aggregation in salt solutions. Proceedings of the National Academy of Sciences of the United States of America. 112: 6766-70. PMID 25964322 DOI: 10.1073/Pnas.1507303112  0.56
2015 Maitra A, Dill KA. Bacterial growth laws reflect the evolutionary importance of energy efficiency. Proceedings of the National Academy of Sciences of the United States of America. 112: 406-11. PMID 25548180 DOI: 10.1073/Pnas.1421138111  1
2015 Presse S, Ghosh K, Lee J, Dill KA. Reply to C. Tsallis' "conceptual inadequacy of the Shore and Johnson axioms for wide classes of complex systems" Entropy. 17: 5043-5046. DOI: 10.3390/E17075043  1
2014 Sharma VK, Patapoff TW, Kabakoff B, Pai S, Hilario E, Zhang B, Li C, Borisov O, Kelley RF, Chorny I, Zhou JZ, Dill KA, Swartz TE. In silico selection of therapeutic antibodies for development: viscosity, clearance, and chemical stability. Proceedings of the National Academy of Sciences of the United States of America. 111: 18601-6. PMID 25512516 DOI: 10.1073/Pnas.1421779112  1
2014 Li L, Fennell CJ, Dill KA. Small molecule solvation changes due to the presence of salt are governed by the cost of solvent cavity formation and dispersion. The Journal of Chemical Physics. 141: 22D518. PMID 25494789 DOI: 10.1063/1.4900890  1
2014 Drechsel NJ, Fennell CJ, Dill KA, Villà-Freixa J. TRIFORCE: Tessellated Semianalytical Solvent Exposed Surface Areas and Derivatives. Journal of Chemical Theory and Computation. 10: 4121-4132. PMID 25221446 DOI: 10.1021/Ct5002818  1
2014 Cohen P, Dill KA, Jaswal SS. Modeling the solvation of nonpolar amino acids in guanidinium chloride solutions. The Journal of Physical Chemistry. B. 118: 10618-23. PMID 25141127 DOI: 10.1021/Jp506379R  1
2014 Dixit PD, Dill KA. Inferring Microscopic Kinetic Rates from Stationary State Distributions. Journal of Chemical Theory and Computation. 10: 3002-3005. PMID 25136269 DOI: 10.1021/Ct5001389  1
2014 Rollins GC, Dill KA. General mechanism of two-state protein folding kinetics. Journal of the American Chemical Society. 136: 11420-7. PMID 25056406 DOI: 10.1021/Ja5049434  1
2014 Perez A, Roy A, Kasavajhala K, Wagaman A, Dill KA, MacCallum JL. Extracting representative structures from protein conformational ensembles. Proteins. 82: 2671-80. PMID 24975328 DOI: 10.1002/Prot.24633  0.44
2014 Pressé S, Peterson J, Lee J, Elms P, MacCallum JL, Marqusee S, Bustamante C, Dill K. Single molecule conformational memory extraction: p5ab RNA hairpin. The Journal of Physical Chemistry. B. 118: 6597-603. PMID 24898871 DOI: 10.1021/Jp500611F  1
2014 Lukši? M, Fennell CJ, Dill KA. Using interpolation for fast and accurate calculation of ion-ion interactions. The Journal of Physical Chemistry. B. 118: 8017-25. PMID 24625086 DOI: 10.1021/Jp501141J  1
2014 Li L, Dill KA, Fennell CJ. Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge. Journal of Computer-Aided Molecular Design. 28: 259-64. PMID 24474161 DOI: 10.1007/S10822-014-9712-8  1
2014 Roy A, Perez A, Dill KA, Maccallum JL. Computing the relative stabilities and the per-residue components in protein conformational changes. Structure (London, England : 1993). 22: 168-75. PMID 24316402 DOI: 10.1016/J.Str.2013.10.015  1
2014 Li L, Fennell CJ, Dill KA. Field-SEA: a model for computing the solvation free energies of nonpolar, polar, and charged solutes in water. The Journal of Physical Chemistry. B. 118: 6431-7. PMID 24299013 DOI: 10.1021/Jp4115139  1
2013 Rocklin GJ, Mobley DL, Dill KA, Hünenberger PH. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects. The Journal of Chemical Physics. 139: 184103. PMID 24320250 DOI: 10.1063/1.4826261  1
2013 Peterson J, Dixit PD, Dill KA. A maximum entropy framework for nonexponential distributions. Proceedings of the National Academy of Sciences of the United States of America. 110: 20380-5. PMID 24297895 DOI: 10.1073/Pnas.1320578110  1
2013 Pressé S, Ghosh K, Lee J, Dill KA. Nonadditive entropies yield probability distributions with biases not warranted by the data. Physical Review Letters. 111: 180604. PMID 24237501 DOI: 10.1103/Physrevlett.111.180604  1
2013 Rocklin GJ, Mobley DL, Dill KA. Calculating the sensitivity and robustness of binding free energy calculations to force field parameters. Journal of Chemical Theory and Computation. 9: 3072-3083. PMID 24015114 DOI: 10.1021/Ct400315Q  1
2013 Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA. Blind prediction of charged ligand binding affinities in a model binding site. Journal of Molecular Biology. 425: 4569-83. PMID 23896298 DOI: 10.1016/J.Jmb.2013.07.030  1
2013 Dill KA. Biophysics. Introduction. Annual Review of Biophysics. 42. PMID 23798065 DOI: 10.1146/annurev-bb-42-050113-100001  1
2013 Rocklin GJ, Mobley DL, Dill KA. Separated topologies--a method for relative binding free energy calculations using orientational restraints. The Journal of Chemical Physics. 138: 085104. PMID 23464180 DOI: 10.1063/1.4792251  1
2013 Kortkhonjia E, Brandman R, Zhou JZ, Voelz VA, Chorny I, Kabakoff B, Patapoff TW, Dill KA, Swartz TE. Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations. Mabs. 5: 306-22. PMID 23396076 DOI: 10.4161/Mabs.23651  1
2013 Pressé S, Lee J, Dill KA. Extracting conformational memory from single-molecule kinetic data. The Journal of Physical Chemistry. B. 117: 495-502. PMID 23259771 DOI: 10.1021/Jp309420U  1
2013 Pressé S, Ghosh K, Lee J, Dill KA. Principles of maximum entropy and maximum caliber in statistical physics Reviews of Modern Physics. 85: 1115-1141. DOI: 10.1103/Revmodphys.85.1115  1
2012 Perez A, Yang Z, Bahar I, Dill KA, MacCallum JL. FlexE: Using elastic network models to compare models of protein structure. Journal of Chemical Theory and Computation. 8: 3985-3991. PMID 25530735 DOI: 10.1021/Ct300148F  1
2012 Urbi? T, Fennell CJ, Dill KA. A microscopic theory of solvation of monoions. Acta Chimica Slovenica. 59: 554-8. PMID 24061310  1
2012 Dill KA, MacCallum JL. The protein-folding problem, 50 years on. Science (New York, N.Y.). 338: 1042-6. PMID 23180855 DOI: 10.1126/Science.1219021  1
2012 Butterfoss GL, Yoo B, Jaworski JN, Chorny I, Dill KA, Zuckermann RN, Bonneau R, Kirshenbaum K, Voelz VA. De novo structure prediction and experimental characterization of folded peptoid oligomers. Proceedings of the National Academy of Sciences of the United States of America. 109: 14320-5. PMID 22908242 DOI: 10.1073/Pnas.1209945109  1
2012 Peterson GJ, Pressé S, Peterson KS, Dill KA. Simulated evolution of protein-protein interaction networks with realistic topology. Plos One. 7: e39052. PMID 22768057 DOI: 10.1371/Journal.Pone.0039052  1
2012 Lukši? M, Urbic T, Hribar-Lee B, Dill KA. Simple model of hydrophobic hydration. The Journal of Physical Chemistry. B. 116: 6177-86. PMID 22564051 DOI: 10.1021/Jp300743A  1
2012 Fennell CJ, Li L, Dill KA. Simple liquid models with corrected dielectric constants. The Journal of Physical Chemistry. B. 116: 6936-44. PMID 22397577 DOI: 10.1021/Jp3002383  1
2012 Ge H, Pressé S, Ghosh K, Dill KA. Markov processes follow from the principle of maximum caliber. The Journal of Chemical Physics. 136: 064108. PMID 22360170 DOI: 10.1063/1.3681941  1
2012 Schmit JD, Dill K. Growth rates of protein crystals. Journal of the American Chemical Society. 134: 3934-7. PMID 22339624 DOI: 10.1021/Ja207336R  1
2012 Kehoe CW, Fennell CJ, Dill KA. Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test. Journal of Computer-Aided Molecular Design. 26: 563-8. PMID 22205387 DOI: 10.1007/S10822-011-9536-8  1
2012 Dill KA, Ghosh K, Schmit J. Reply to Vazquez: Optimal density is robust to variations in calculation Proceedings of the National Academy of Sciences of the United States of America. 109: E534. DOI: 10.1073/Pnas.1121337109  1
2011 Fennell CJ, Dill KA. Physical Modeling of Aqueous Solvation. Journal of Statistical Physics. 145: 209-226. PMID 25143658 DOI: 10.1007/S10955-011-0232-9  1
2011 MacCallum JL, Pérez A, Schnieders MJ, Hua L, Jacobson MP, Dill KA. Assessment of protein structure refinement in CASP9. Proteins. 79: 74-90. PMID 22069034 DOI: 10.1002/Prot.23131  1
2011 Dill KA, Ghosh K, Schmit JD. Physical limits of cells and proteomes. Proceedings of the National Academy of Sciences of the United States of America. 108: 17876-82. PMID 22006304 DOI: 10.1073/Pnas.1114477108  1
2011 Schmit JD, Whitelam S, Dill K. Electrostatics and aggregation: how charge can turn a crystal into a gel. The Journal of Chemical Physics. 135: 085103. PMID 21895221 DOI: 10.1063/1.3626803  1
2011 Pressé S, Ghosh K, Dill KA. Modeling stochastic dynamics in biochemical systems with feedback using maximum caliber. The Journal of Physical Chemistry. B. 115: 6202-12. PMID 21524067 DOI: 10.1021/Jp111112S  1
2011 Fennell CJ, Kehoe CW, Dill KA. Modeling aqueous solvation with semi-explicit assembly. Proceedings of the National Academy of Sciences of the United States of America. 108: 3234-9. PMID 21300905 DOI: 10.1073/Pnas.1017130108  1
2011 Schmit JD, Ghosh K, Dill K. What drives amyloid molecules to assemble into oligomers and fibrils? Biophysical Journal. 100: 450-8. PMID 21244841 DOI: 10.1016/J.Bpj.2010.11.041  1
2011 Voelz VA, Dill KA, Chorny I. Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER. Biopolymers. 96: 639-50. PMID 21184487 DOI: 10.1002/Bip.21575  1
2010 Pressé S, Ghosh K, Phillips R, Dill KA. Dynamical fluctuations in biochemical reactions and cycles. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 82: 031905. PMID 21230106 DOI: 10.1103/Physreve.82.031905  1
2010 Ghosh K, Dill K. Cellular proteomes have broad distributions of protein stability Biophysical Journal. 99: 3996-4002. PMID 21156142 DOI: 10.1016/J.Bpj.2010.10.036  1
2010 Hribar-Lee B, Dill KA, Vlachy V. Receptacle model of salting-in by tetramethylammonium ions. The Journal of Physical Chemistry. B. 114: 15085-91. PMID 21028768 DOI: 10.1021/Jp108052R  1
2010 Peterson GJ, Pressé S, Dill KA. Nonuniversal power law scaling in the probability distribution of scientific citations. Proceedings of the National Academy of Sciences of the United States of America. 107: 16023-7. PMID 20805513 DOI: 10.1073/Pnas.1010757107  1
2010 Urbic T, Dill KA. A statistical mechanical theory for a two-dimensional model of water. The Journal of Chemical Physics. 132: 224507. PMID 20550408 DOI: 10.1063/1.3454193  1
2010 Kalyuzhnyi YV, Vlachy V, Dill KA. Aqueous alkali halide solutions: can osmotic coefficients be explained on the basis of the ionic sizes alone? Physical Chemistry Chemical Physics : Pccp. 12: 6260-6. PMID 20405084 DOI: 10.1039/B924735A  1
2010 Schmit JD, Dill KA. The stabilities of protein crystals. The Journal of Physical Chemistry. B. 114: 4020-7. PMID 20199035 DOI: 10.1021/Jp9107188  1
2010 Fennell CJ, Kehoe C, Dill KA. Oil/water transfer is partly driven by molecular shape, not just size. Journal of the American Chemical Society. 132: 234-40. PMID 19961159 DOI: 10.1021/Ja906399E  1
2009 Hribar-Lee B, Vlachy V, Dill KA. Modeling Hofmeister Effects. Acta Chimica Slovenica. 56: 196-202. PMID 20161468  1
2009 Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations. Journal of Chemical Theory and Computation. 5: 350-358. PMID 20150953 DOI: 10.1021/Ct800409D  1
2009 Bizjak A, Urbic T, Vlachy V, Dill KA. Theory for the three-dimensional Mercedes-Benz model of water. The Journal of Chemical Physics. 131: 194504. PMID 19929057 DOI: 10.1063/1.3259970  1
2009 Fennell CJ, Bizjak A, Vlachy V, Dill KA, Sarupria S, Rajamani S, Garde S. Ion pairing in molecular simulations of aqueous alkali halide solutions. The Journal of Physical Chemistry. B. 113: 14837-8. PMID 19807139 DOI: 10.1021/jp908484v  0.6
2009 Druchok M, Vlachy V, Dill KA. Computer simulations of ionenes, hydrophobic ions with unusual solution thermodynamic properties. The ion-specific effects. The Journal of Physical Chemistry. B. 113: 14270-6. PMID 19799433 DOI: 10.1021/Jp906727H  1
2009 Wu D, Ghosh K, Inamdar M, Lee HJ, Fraser S, Dill K, Phillips R. Trajectory approach to two-state kinetics of single particles on sculpted energy landscapes. Physical Review Letters. 103: 050603. PMID 19792475 DOI: 10.1103/Physrevlett.103.050603  1
2009 Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill KA, Shoichet BK. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. Journal of Molecular Biology. 394: 747-63. PMID 19782087 DOI: 10.1016/J.Jmb.2009.09.049  1
2009 MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson MP, Dill KA. Assessment of the protein-structure refinement category in CASP8. Proteins. 77: 66-80. PMID 19714776 DOI: 10.1002/Prot.22538  1
2009 Ghosh K, Dill KA. Computing protein stabilities from their chain lengths. Proceedings of the National Academy of Sciences of the United States of America. 106: 10649-54. PMID 19541647 DOI: 10.1073/Pnas.0903995106  1
2009 Mobley DL, Dill KA. Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Structure (London, England : 1993). 17: 489-98. PMID 19368882 DOI: 10.1016/J.Str.2009.02.010  1
2009 Druchok M, Vlachy V, Dill KA. Explicit-water molecular dynamics study of a short-chain 3,3 ionene in solutions with sodium halides. The Journal of Chemical Physics. 130: 134903. PMID 19355776 DOI: 10.1063/1.3078268  1
2009 Mobley DL, Bayly CI, Cooper MD, Dill KA. Predictions of hydration free energies from all-atom molecular dynamics simulations. The Journal of Physical Chemistry. B. 113: 4533-7. PMID 19271713 DOI: 10.1021/Jp806838B  1
2009 Fennell CJ, Bizjak A, Vlachy V, Dill KA. Ion pairing in molecular simulations of aqueous alkali halide solutions. The Journal of Physical Chemistry. B. 113: 6782-91. PMID 19206510 DOI: 10.1021/Jp809782Z  1
2009 Voelz VA, Shell MS, Dill KA. Predicting peptide structures in native proteins from physical simulations of fragments. Plos Computational Biology. 5: e1000281. PMID 19197352 DOI: 10.1371/Journal.Pcbi.1000281  1
2009 Shell MS, Ozkan SB, Voelz V, Wu GA, Dill KA. Blind test of physics-based prediction of protein structures. Biophysical Journal. 96: 917-24. PMID 19186130 DOI: 10.1016/J.Bpj.2008.11.009  1
2009 Ghosh K, Dill KA. Theory for protein folding cooperativity: helix bundles. Journal of the American Chemical Society. 131: 2306-12. PMID 19170581 DOI: 10.1021/Ja808136X  1
2009 Watkins GA, Jones EF, Scott Shell M, VanBrocklin HF, Pan MH, Hanrahan SM, Feng JJ, He J, Sounni NE, Dill KA, Contag CH, Coussens LM, Franc BL. Development of an optimized activatable MMP-14 targeted SPECT imaging probe. Bioorganic & Medicinal Chemistry. 17: 653-9. PMID 19109023 DOI: 10.1016/J.Bmc.2008.11.078  1
2008 Urbi? T, Urbi? T, Avbelj F, Dill KA. Molecular Simulations Find Stable Structures in Fragments of Protein G. Acta Chimica Slovenica. 2008: 385-395. PMID 20448839  1
2008 Wu GA, Coutsias EA, Dill KA. Iterative assembly of helical proteins by optimal hydrophobic packing. Structure (London, England : 1993). 16: 1257-66. PMID 18682227 DOI: 10.1016/J.Str.2008.04.019  1
2008 Lee BC, Chu TK, Dill KA, Zuckermann RN. Biomimetic nanostructures: creating a high-affinity zinc-binding site in a folded nonbiological polymer. Journal of the American Chemical Society. 130: 8847-55. PMID 18597438 DOI: 10.1021/Ja802125X  1
2008 Dill KA, Ozkan SB, Shell MS, Weikl TR. The protein folding problem. Annual Review of Biophysics. 37: 289-316. PMID 18573083 DOI: 10.1063/1.881371  1
2008 Stock G, Ghosh K, Dill KA. Maximum Caliber: a variational approach applied to two-state dynamics. The Journal of Chemical Physics. 128: 194102. PMID 18500851 DOI: 10.1063/1.2918345  1
2008 Shell MS, Ritterson R, Dill KA. A test on peptide stability of AMBER force fields with implicit solvation. The Journal of Physical Chemistry. B. 112: 6878-86. PMID 18471007 DOI: 10.1021/Jp800282X  1
2008 Mobley DL, Baker JR, Barber AE, Fennell CJ, Dill KA. Charge asymmetries in hydration of polar solutes. The Journal of Physical Chemistry. B. 112: 2405-14. PMID 18251538 DOI: 10.1021/Jp709958F  1
2008 Mobley DL, Dill KA, Chodera JD. Treating entropy and conformational changes in implicit solvent simulations of small molecules. The Journal of Physical Chemistry. B. 112: 938-46. PMID 18171044 DOI: 10.1021/Jp0764384  1
2008 Dill KA. The second law and biology Aip Conference Proceedings. 1033: 90-110. DOI: 10.1063/1.2979068  1
2007 Chodera JD, Swope WC, Pitera JW, Seok C, Dill KA. Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations. Journal of Chemical Theory and Computation. 3: 26-41. PMID 26627148 DOI: 10.1021/Ct0502864  1
2007 Mobley DL, Chodera JD, Dill KA. The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change. Journal of Chemical Theory and Computation. 3: 1231-1235. PMID 18843379 DOI: 10.1021/Ct700032N  1
2007 Urbic T, Vlachy V, Kalyuzhnyi YV, Dill KA. An improved thermodynamic perturbation theory for Mercedes-Benz water. The Journal of Chemical Physics. 127: 174511. PMID 17994831 DOI: 10.1063/1.2784124  1
2007 Urbic T, Vlachy V, Kalyuzhnyi YV, Dill KA. Theory for the solvation of nonpolar solutes in water. The Journal of Chemical Physics. 127: 174505. PMID 17994825 DOI: 10.1063/1.2779329  1
2007 Ghosh K, Ozkan SB, Dill KA. The ultimate speed limit to protein folding is conformational searching. Journal of the American Chemical Society. 129: 11920-7. PMID 17824609 DOI: 10.1021/Ja066785B  1
2007 Ozkan SB, Wu GA, Chodera JD, Dill KA. Protein folding by zipping and assembly. Proceedings of the National Academy of Sciences of the United States of America. 104: 11987-92. PMID 17620603 DOI: 10.1073/Pnas.0703700104  1
2007 Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA. Predicting absolute ligand binding free energies to a simple model site. Journal of Molecular Biology. 371: 1118-34. PMID 17599350 DOI: 10.1016/J.Jmb.2007.06.002  1
2007 Dill KA, Ozkan SB, Weikl TR, Chodera JD, Voelz VA. The protein folding problem: when will it be solved? Current Opinion in Structural Biology. 17: 342-6. PMID 17572080 DOI: 10.1016/J.Sbi.2007.06.001  1
2007 Bradford JA, Dill KA. Stochastic innovation as a mechanism by which catalysts might self-assemble into chemical reaction networks. Proceedings of the National Academy of Sciences of the United States of America. 104: 10098-103. PMID 17548812 DOI: 10.1073/Pnas.0703522104  1
2007 Chodera JD, Singhal N, Pande VS, Dill KA, Swope WC. Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. The Journal of Chemical Physics. 126: 155101. PMID 17461665 DOI: 10.1063/1.2714538  1
2007 Lucas A, Huang L, Joshi A, Dill KA. Statistical mechanics of helix bundles using a dynamic programming approach. Journal of the American Chemical Society. 129: 4272-81. PMID 17362002 DOI: 10.1021/Ja067153S  1
2007 Mobley DL, Dumont E, Chodera JD, Dill KA. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. The Journal of Physical Chemistry. B. 111: 2242-54. PMID 17291029 DOI: 10.1021/Jp0667442  1
2007 Voelz VA, Dill KA. Exploring zipping and assembly as a protein folding principle. Proteins. 66: 877-88. PMID 17154424 DOI: 10.1002/Prot.21234  1
2007 Weikl TR, Dill KA. Transition-states in protein folding kinetics: the structural interpretation of Phi values. Journal of Molecular Biology. 365: 1578-86. PMID 17141267 DOI: 10.1016/J.Jmb.2006.10.082  1
2007 Hockenmaier J, Joshi AK, Dill KA. Routes are trees: the parsing perspective on protein folding. Proteins. 66: 1-15. PMID 17063473 DOI: 10.1002/Prot.21195  1
2007 Chodera JD, Swope WC, Pitera JW, Seok C, Dill KA. Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations Journal of Chemical Theory and Computation. 3: 26-41. DOI: 10.1021/ct0502864  1
2007 Dill KA, Lucas A, Hockenmaier J, Huang L, Chiang D, Joshi AK. Computational linguistics: A new tool for exploring biopolymer structures and statistical mechanics Polymer. 48: 4289-4300. DOI: 10.1016/J.Polymer.2007.05.018  1
2007 Bizjak A, Urbič T, Vlachy V, Dill KA. The three-dimensional "Mercedes Benz" model of water Acta Chimica Slovenica. 54: 532-537.  1
2006 Ghosh K, Dill KA, Inamdar MM, Seitaridou E, Phillips R. Teaching the principles of statistical dynamics. American Journal of Physics. 74: 123-133. PMID 23585693 DOI: 10.1119/1.2142789  1
2006 Mobley DL, Chodera JD, Dill KA. On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. The Journal of Chemical Physics. 125: 084902. PMID 16965052 DOI: 10.1063/1.2221683  1
2006 Ho BK, Dill KA. Folding very short peptides using molecular dynamics. Plos Computational Biology. 2: e27. PMID 16617376 DOI: 10.1371/Journal.Pcbi.0020027  1
2006 Urbic T, Vlachy V, Dill KA. Confined water: a Mercedes-Benz model study. The Journal of Physical Chemistry. B. 110: 4963-70. PMID 16526737 DOI: 10.1021/Jp055543F  1
2006 Chiang D, Joshi AK, Dill KA. A grammatical theory for the conformational changes of simple helix bundles. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 13: 21-42. PMID 16472020 DOI: 10.1089/Cmb.2006.13.21  1
2006 Chodera JD, Swope WC, Pitera JW, Dill KA. Long-time protein folding dynamics from short-time molecular dynamics simulations Multiscale Modeling and Simulation. 5: 1214-1226. DOI: 10.1137/06065146X  1
2006 Coutsias EA, Seok C, Wester MJ, Dill KA. Resultants and loop closure International Journal of Quantum Chemistry. 106: 176-189. DOI: 10.1002/Qua.20751  1
2006 Hockenmaier J, Joshi AK, Dill KA. Protein folding and chart parsing Coling/Acl 2006 - Emnlp 2006: 2006 Conference On Empirical Methods in Natural Language Processing, Proceedings of the Conference. 293-300.  1
2006 Hribar-Lee B, Dill KA. Modeling simple alcohols in two dimensions Acta Chimica Slovenica. 53: 257-263.  1
2005 Chorny I, Dill KA, Jacobson MP. Surfaces affect ion pairing. The Journal of Physical Chemistry. B. 109: 24056-60. PMID 16375397 DOI: 10.1021/Jp055043M  1
2005 Xu H, Dill KA. Water's hydrogen bonds in the hydrophobic effect: a simple model. The Journal of Physical Chemistry. B. 109: 23611-7. PMID 16375338 DOI: 10.1021/Jp0526750  1
2005 Coutsias EA, Seok C, Dill KA. Rotational superposition and least squares: the SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller. Journal of Computational Chemistry. 26: 1663-5. PMID 16175579 DOI: 10.1002/Jcc.20316  1
2005 Lee BC, Zuckermann RN, Dill KA. Folding a nonbiological polymer into a compact multihelical structure. Journal of the American Chemical Society. 127: 10999-1009. PMID 16076207 DOI: 10.1021/Ja0514904  1
2005 Merlo C, Dill KA, Weikl TR. Phi values in protein-folding kinetics have energetic and structural components. Proceedings of the National Academy of Sciences of the United States of America. 102: 10171-5. PMID 16009941 DOI: 10.1073/Pnas.0504171102  1
2005 Dill KA, Truskett TM, Vlachy V, Hribar-Lee B. Modeling water, the hydrophobic effect, and ion solvation. Annual Review of Biophysics and Biomolecular Structure. 34: 173-99. PMID 15869376 DOI: 10.1146/Annurev.Biophys.34.040204.144517  1
2005 Ho BK, Coutsias EA, Seok C, Dill KA. The flexibility in the proline ring couples to the protein backbone. Protein Science : a Publication of the Protein Society. 14: 1011-8. PMID 15772308 DOI: 10.1110/Ps.041156905  1
2005 Jaswal SS, Truhlar SM, Dill KA, Agard DA. Comprehensive analysis of protein folding activation thermodynamics reveals a universal behavior violated by kinetically stable proteases. Journal of Molecular Biology. 347: 355-66. PMID 15740746 DOI: 10.1016/J.Jmb.2005.01.032  1
2004 Coutsias EA, Seok C, Dill KA. Using quaternions to calculate RMSD. Journal of Computational Chemistry. 25: 1849-57. PMID 15376254 DOI: 10.1002/Jcc.20110  1
2004 Horn T, Lee BC, Dill KA, Zuckermann RN. Incorporation of chemoselective functionalities into peptoids via solid-phase submonomer synthesis. Bioconjugate Chemistry. 15: 428-35. PMID 15025542 DOI: 10.1021/Bc0341831  1
2004 Weikl TR, Palassini M, Dill KA. Cooperativity in two-state protein folding kinetics. Protein Science : a Publication of the Protein Society. 13: 822-9. PMID 14978313 DOI: 10.1110/Ps.03403604  1
2004 Coutsias EA, Seok C, Jacobson MP, Dill KA. A kinematic view of loop closure. Journal of Computational Chemistry. 25: 510-28. PMID 14735570 DOI: 10.1002/Jcc.10416  1
2004 Urbic T, Vlachy V, Pizio O, Dill KA. Water-like fluid in the presence of Lennard-Jones obstacles: Predictions of an associative replica Ornstein-Zernike theory Journal of Molecular Liquids. 112: 71-80. DOI: 10.1016/J.Molliq.2003.12.001  1
2004 Vlachy V, Hribar-Lee B, Kalyuzhnyi YV, Dill KA. Short-range interactions: From simple ions to polyelectrolyte solutions Current Opinion in Colloid and Interface Science. 9: 128-132. DOI: 10.1016/J.Cocis.2004.05.017  1
2003 Wu CW, Kirshenbaum K, Sanborn TJ, Patch JA, Huang K, Dill KA, Zuckermann RN, Barron AE. Structural and spectroscopic studies of peptoid oligomers with alpha-chiral aliphatic side chains. Journal of the American Chemical Society. 125: 13525-30. PMID 14583049 DOI: 10.1021/Ja037540R  1
2003 Schonbrun J, Dill KA. Fast protein folding kinetics. Proceedings of the National Academy of Sciences of the United States of America. 100: 12678-82. PMID 14569019 DOI: 10.1073/Pnas.1735417100  1
2003 Truskett TM, Dill KA. A simple analytical model of water. Biophysical Chemistry. 105: 449-59. PMID 14499910 DOI: 10.1016/S0301-4622(03)00107-8  1
2003 Weikl TR, Dill KA. Folding kinetics of two-state proteins: effect of circularization, permutation, and crosslinks. Journal of Molecular Biology. 332: 953-63. PMID 12972264 DOI: 10.1016/S0022-2836(03)00884-2  1
2003 Amato NM, Dill KA, Song G. Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 239-55. PMID 12935327 DOI: 10.1089/10665270360688002  1
2003 Weikl TR, Dill KA. Folding rates and low-entropy-loss routes of two-state proteins. Journal of Molecular Biology. 329: 585-98. PMID 12767836 DOI: 10.1016/S0022-2836(03)00436-4  1
2003 Song G, Thomas S, Dill KA, Scholtz JM, Amato NM. A path planning-based study of protein folding with a case study of hairpin formation in protein G and L. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 240-51. PMID 12603032  1
2003 Ozkan SB, Dill KA, Bahar I. Computing the transition state populations in simple protein models. Biopolymers. 68: 35-46. PMID 12579578 DOI: 10.1002/Bip.10280  1
2003 Seok C, Rosen JB, Chodera JD, Dill KA. MOPED: method for optimizing physical energy parameters using decoys. Journal of Computational Chemistry. 24: 89-97. PMID 12483678 DOI: 10.1002/Jcc.10124  1
2003 Lucas A, Dill KA. Statistical mechanics of pseudoknot polymers Journal of Chemical Physics. 119: 2414-2421. DOI: 10.1063/1.1587129  1
2003 Urbič T, Vlachy V, Kalyuzhnyi YV, Dill KA. Orientation-dependent integral equation theory for a two-dimensional model of water Journal of Chemical Physics. 118: 5516-5525. DOI: 10.1063/1.1556754  1
2002 Southall NT, Dill KA. Potential of mean force between two hydrophobic solutes in water. Biophysical Chemistry. 101: 295-307. PMID 12488009 DOI: 10.1016/S0301-4622(02)00167-9  1
2002 Hribar B, Southall NT, Vlachy V, Dill KA. How ions affect the structure of water. Journal of the American Chemical Society. 124: 12302-11. PMID 12371874 DOI: 10.1021/Ja026014H  1
2002 Ozkan SB, Dill KA, Bahar I. Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model. Protein Science : a Publication of the Protein Society. 11: 1958-70. PMID 12142450 DOI: 10.1110/Ps.0207102  1
2002 Ball KD, Erman B, Dill KA. The elastic net algorithm and protein structure prediction. Journal of Computational Chemistry. 23: 77-83. PMID 11913391 DOI: 10.1002/Jcc.1158  1
2002 Truskett TM, Dill KA. Predicting water's phase diagram and liquid-state anomalies Journal of Chemical Physics. 117: 5101-5104. DOI: 10.1063/1.1505438  1
2002 Urbi T, Vlachy V, Kalyuzhnyi YV, Southall NT, Dill KA. A two-dimensional model of water: Solvation of nonpolar solutes Journal of Chemical Physics. 116: 723-729. DOI: 10.1063/1.1427307  1
2002 Truskett TM, Dill KA. A simple statistical mechanical model of water Journal of Physical Chemistry B. 106: 11829-11842. DOI: 10.1021/Jp021418H  1
2002 Southall NT, Dill KA, Haymet ADJ. A view of the hydrophobic effect Journal of Physical Chemistry B. 106: 521-533. DOI: 10.1021/Jp015514E  1
2001 Zhou HX, Dill KA. Stabilization of proteins in confined spaces. Biochemistry. 40: 11289-93. PMID 11560476 DOI: 10.1021/Bi0155504  1
2001 Ozkan SB, Bahar I, Dill KA. Transition states and the meaning of Phi-values in protein folding kinetics. Nature Structural Biology. 8: 765-9. PMID 11524678 DOI: 10.1038/Nsb0901-765  1
2001 Liang J, Dill KA. Are proteins well-packed? Biophysical Journal. 81: 751-66. PMID 11463623 DOI: 10.1016/S0006-3495(01)75739-6  1
2001 Silverstein KAT, Dill KA, Haymet ADJ. Hydrophobicity in a simple model of water: Entropy penalty as a sum of competing terms via full, angular expansion Journal of Chemical Physics. 114: 6303-6314. DOI: 10.1063/1.1355997  1
2001 Tøstesen E, Chen ASJ, Dill KA. RNA folding transitions and cooperativity Journal of Physical Chemistry B. 105: 1618-1630. DOI: 10.1021/Jp002877Q  1
2001 Kalyuzhnyi YV, Vlachy V, Dill KA. Hydration of simple ions. Effect of the charge density Acta Chimica Slovenica. 48: 309-316.  1
2000 Rosen JB, Phillips AT, Oh SY, Dill KA. A method for parameter optimization in computational biology. Biophysical Journal. 79: 2818-24. PMID 11106591 DOI: 10.1016/S0006-3495(00)76520-9  1
2000 Yue K, Dill KA. Constraint-based assembly of tertiary protein structures from secondary structure elements. Protein Science : a Publication of the Protein Society. 9: 1935-46. PMID 11106167  1
2000 Chen SJ, Dill KA. RNA folding energy landscapes. Proceedings of the National Academy of Sciences of the United States of America. 97: 646-51. PMID 10639133 DOI: 10.1073/Pnas.97.2.646  1
2000 Urbič T, Vlachy V, Kalyuzhnyi YV, Southall NT, Dill KA. A two-dimensional model of water: Theory and computer simulations Journal of Chemical Physics. 112: 2843-2848. DOI: 10.1063/1.480928  1
2000 Wang T, Miller J, Wingreen NS, Tang C, Dill KA. Symmetry and designability for lattice protein models Journal of Chemical Physics. 113: 8329-8336. DOI: 10.1063/1.1315324  1
2000 Southall NT, Dill KA. The mechanism of hydrophobic solvation depends on solute radius Journal of Physical Chemistry B. 104: 1326-1331. DOI: 10.1021/Jp992860B  1
2000 Brem R, Chan HS, Dill KA. Extracting microscopic energies from oil-phase solvation experiments Journal of Physical Chemistry B. 104: 7471-7482. DOI: 10.1021/Jp0003297  1
2000 Silverstein KAT, Haymet ADJ, Dill KA. The strength of hydrogen bonds in liquid water and around nonpolar solutes Journal of the American Chemical Society. 122: 8037-8041. DOI: 10.1021/Ja000459T  1
1999 Young M, Kirshenbaum K, Dill KA, Highsmith S. Predicting conformational switches in proteins. Protein Science : a Publication of the Protein Society. 8: 1752-64. PMID 10493576 DOI: 10.1110/Ps.8.9.1752  1
1999 Kirshenbaum K, Zuckermann RN, Dill KA. Designing polymers that mimic biomolecules. Current Opinion in Structural Biology. 9: 530-5. PMID 10449369 DOI: 10.1016/S0959-440X(99)80075-X  1
1999 Dill KA. Strengthening biomedicine's roots. Nature. 400: 309-10. PMID 10432104 DOI: 10.1038/22415  1
1999 Dill KA. Polymer principles and protein folding. Protein Science : a Publication of the Protein Society. 8: 1166-80. PMID 10386867 DOI: 10.1110/Ps.8.6.1166  1
1999 Brem R, Dill KA. The effect of multiple binding modes on empirical modeling of ligand docking to proteins. Protein Science : a Publication of the Protein Society. 8: 1134-43. PMID 10338024 DOI: 10.1110/Ps.8.5.1134  1
1999 Ishikawa K, Yue K, Dill KA. Predicting the structures of 18 peptides using Geocore. Protein Science : a Publication of the Protein Society. 8: 716-21. PMID 10211817 DOI: 10.1110/Ps.8.4.716  1
1999 Silverstein KAT, Haymet ADJ, Dill KA. Molecular model of hydrophobic solvation Journal of Chemical Physics. 111: 8000-8009. DOI: 10.1063/1.480133  1
1999 Foreman KW, Phillips AT, Rosen JB, Dill KA. Comparing search strategies for finding global optima on energy landscapes Journal of Computational Chemistry. 20: 1527-1532. DOI: 10.1002/(Sici)1096-987X(19991115)20:14<1527::Aid-Jcc5>3.0.Co;2-W  1
1999 Tang KES, Dill KA. How Experiments See Fluctuations of Native Proteins: Perspective from an Exact Model International Journal of Quantum Chemistry. 75: 147-164.  1
1998 Tang KE, Dill KA. Native protein fluctuations: the conformational-motion temperature and the inverse correlation of protein flexibility with protein stability. Journal of Biomolecular Structure & Dynamics. 16: 397-411. PMID 9833677 DOI: 10.1080/07391102.1998.10508256  1
1998 Armand P, Kirshenbaum K, Goldsmith RA, Farr-Jones S, Barron AE, Truong KT, Dill KA, Mierke DF, Cohen FE, Zuckermann RN, Bradley EK. NMR determination of the major solution conformation of a peptoid pentamer with chiral side chains. Proceedings of the National Academy of Sciences of the United States of America. 95: 4309-14. PMID 9539733 DOI: 10.1073/Pnas.95.8.4309  1
1998 Kirshenbaum K, Barron AE, Goldsmith RA, Armand P, Bradley EK, Truong KT, Dill KA, Cohen FE, Zuckermann RN. Sequence-specific polypeptoids: a diverse family of heteropolymers with stable secondary structure. Proceedings of the National Academy of Sciences of the United States of America. 95: 4303-8. PMID 9539732 DOI: 10.1073/Pnas.95.8.4303  1
1998 Chan HS, Dill KA. Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics. Proteins. 30: 2-33. PMID 9443337 DOI: 10.1002/(Sici)1097-0134(19980101)30:1<2::Aid-Prot2>3.0.Co;2-R  1
1998 Chen SJ, Dill KA. Theory for the conformational changes of double-stranded chain molecules Journal of Chemical Physics. 109: 4602-4616. DOI: 10.1063/1.477065  1
1998 DeVido DR, Dorsey JG, Chan HS, Dill KA. Oil/water partitioning has a different thermodynamic signature when the oil solvent chains are aligned than when they are amorphous Journal of Physical Chemistry B. 102: 7272-7279. DOI: 10.1021/Jp9807165  1
1998 Silverstein KAT, Haymet ADJ, Dill KA. A simple model of water and the hydrophobic effect Journal of the American Chemical Society. 120: 3166-3175. DOI: 10.1021/Ja973029K  1
1998 Silverstein KAT, Dill KA, Haymet ADJ. Hydrophobicity in a simple model of water: Solvation and hydrogen bond energies Fluid Phase Equilibria. 150: 83-90. DOI: 10.1016/S0378-3812(98)00278-7  1
1997 Armand P, Kirshenbaum K, Falicov A, Dunbrack RL, Dill KA, Zuckermann RN, Cohen FE. Chiral N-substituted glycines can form stable helical conformations. Folding & Design. 2: 369-75. PMID 9427011 DOI: 10.1016/S1359-0278(97)00051-5  1
1997 Miller DW, Dill KA. Ligand binding to proteins: the binding landscape model. Protein Science : a Publication of the Protein Society. 6: 2166-79. PMID 9336839 DOI: 10.1002/Pro.5560061011  1
1997 Dill KA, Phillips AT, Rosen JB. Protein structure and energy landscape dependence on sequence using a continuous energy function. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 4: 227-39. PMID 9278057 DOI: 10.1089/Cmb.1997.4.227  1
1997 Chan HS, Dill KA. Solvation: How to obtain microscopic energies from partitioning and solvation experiments Annual Review of Biophysics and Biomolecular Structure. 26: 425-459. PMID 9241426 DOI: 10.1146/Annurev.Biophys.26.1.425  1
1997 Dill KA. Additivity principles in biochemistry Journal of Biological Chemistry. 272: 701-704. PMID 8995351 DOI: 10.1074/Jbc.272.2.701  1
1997 Dill KA, Chan HS. From levinthal to pathways to funnels Nature Structural Biology. 4: 10-19. PMID 8989315 DOI: 10.1038/Nsb0197-10  1
1997 Dill KA. Protein folding froh the perspective of simple models Faseb Journal. 11: A1292.  1
1996 Thomas PD, Dill KA. An iterative method for extracting energy-like quantities from protein structures Proceedings of the National Academy of Sciences of the United States of America. 93: 11628-11633. PMID 8876187 DOI: 10.1073/Pnas.93.21.11628  1
1996 Chan HS, Dill KA. A simple model of chaperonin-mediated protein folding. Proteins. 24: 345-51. PMID 8778781 DOI: 10.1002/(Sici)1097-0134(199603)24:3<345::Aid-Prot7>3.0.Co;2-F  0.36
1996 Chan HS, Dill KA. Comparing folding codes for proteins and polymers. Proteins. 24: 335-44. PMID 8778780 DOI: 10.1002/(Sici)1097-0134(199603)24:3<335::Aid-Prot6>3.0.Co;2-F  0.44
1996 Yue K, Dill KA. Folding proteins with a simple energy function and extensive conformational searching Protein Science. 5: 254-261. PMID 8745403 DOI: 10.1002/Pro.5560050209  1
1996 Chen SJ, Dill KA. Symmetries in proteins: A knot theory approach Journal of Chemical Physics. 104: 5964-5973. DOI: 10.1063/1.471328  1
1996 Haymet ADJ, Silverstein KAT, Dill KA. Hydrophobicity reinterpreted as 'minimisation of the entropy penalty of solvation' Faraday Discussions. 103: 117-124. DOI: 10.1039/Fd9960300117  1
1996 Wallace DG, Dill KA. Treating sequence dependence of protein stability in a mean-field model Biopolymers. 39: 115-127. DOI: 10.1002/(Sici)1097-0282(199607)39:1<115::Aid-Bip12>3.0.Co;2-F  1
1995 Sun S, Brem R, Chan HS, Dill KA. Designing amino acid sequences to fold with good hydrophobic cores. Protein Engineering. 8: 1205-13. PMID 8869633 DOI: 10.1093/Protein/8.12.1205  1
1995 Yue K, Dill KA. Forces of tertiary structural organization in globular proteins Proceedings of the National Academy of Sciences of the United States of America. 92: 146-150. PMID 7816806 DOI: 10.1073/Pnas.92.1.146  1
1995 Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, Thomas PD, Chan HS. Principles of protein folding--a perspective from simple exact models. Protein Science : a Publication of the Protein Society. 4: 561-602. PMID 7613459 DOI: 10.1002/Pro.5560040401  0.32
1994 Lattman EE, Fiebig KM, Dill KA. Modeling compact denatured states of proteins Biochemistry. 33: 6158-6166. PMID 8193129 DOI: 10.1021/Bi00186A015  1
1992 Yue K, Dill KA. Inverse protein folding problem: Designing polymer sequences Proceedings of the National Academy of Sciences of the United States of America. 89: 4163-4167. PMID 1570343 DOI: 10.1073/Pnas.89.9.4163  1
1992 Cole LA, Dorsey JG, Dill KA. Temperature dependence of retention in reversed-phase liquid chromatography. 2. Mobile-phase considerations. Analytical Chemistry. 64: 1324-7. PMID 1503213 DOI: 10.1021/ac00037a005  1
1992 Shortle D, Hue Sun Chan, Dill KA. Modeling the effects of mutations on the denatured states of proteins Protein Science. 1: 201-215. PMID 1304903 DOI: 10.1002/Pro.5560010202  1
1991 Chan HS, Dill KA. Polymer principles in protein structure and stability. Annual Review of Biophysics and Biophysical Chemistry. 20: 447-90. PMID 1867723 DOI: 10.1146/annurev.bb.20.060191.002311  0.52
1990 Chan HS, Dill KA. Origins of structure in globular proteins. Proceedings of the National Academy of Sciences of the United States of America. 87: 6388-92. PMID 2385597 DOI: 10.1073/Pnas.87.16.6388  0.68
1990 Lau KF, Dill KA. Theory for protein mutability and biogenesis. Proceedings of the National Academy of Sciences of the United States of America. 87: 638-42. PMID 2300551 DOI: 10.1073/Pnas.87.2.638  1
1990 Dill KA, Privalov PL, Gill SJ, Murphy KP. The meaning of hydrophobicity Science. 250: 297-298. PMID 2218535 DOI: 10.1126/Science.2218535  1
1989 Ying PT, Dorsey JG, Dill KA. Retention mechanisms of reversed-phase liquid chromatography: determination of solute-solvent interaction free energies. Analytical Chemistry. 61: 2540-6. PMID 2817406 DOI: 10.1021/Ac00197A017  1
1989 Dill KA, Alonso DOV, Hutchinson K. Thermal stabilities of globular proteins Biochemistry. 28: 5439-5449. PMID 2775715 DOI: 10.1021/Bi00439A019  1
1986 Cantor RS, Dill KA. Theory for the equation of state of phospholipid monolayers Langmuir. 2: 331-337. DOI: 10.1021/La00069A015  1
1984 Dill KA, Koppel DE, Cantor RS. Molecular conformations in surfactant micelles Nature. 309: 42-45. DOI: 10.1038/309042A0  1
1984 Flory PJ, Yoon DY, Dill KA. The interphase in lamellar semicrystalline polymers Macromolecules. 17: 862-868. DOI: 10.1021/Ma00134A055  1
1984 Cantor RS, Dill KA. Statistical thermodynamics of short-chain molecule interphases. 2. Configurational properties of amphiphilic aggregates Macromolecules. 17: 384-388. DOI: 10.1021/Ma00133A023  1
1984 Dill KA, Cantor RS. Statistical thermodynamics of short-chain molecule interphases. 1. Theory Macromolecules. 17: 380-384. DOI: 10.1021/Ma00133A022  1
1981 Dill KA, Flory PJ. Molecular organization in micelles and vesicles. Proceedings of the National Academy of Sciences of the United States of America. 78: 676-80. PMID 16592970 DOI: 10.1073/Pnas.78.2.676  1
1980 Dill KA, Flory PJ. Interphases of chain molecules: Monolayers and lipid bilayer membranes. Proceedings of the National Academy of Sciences of the United States of America. 77: 3115-9. PMID 16592834 DOI: 10.1073/Pnas.77.6.3115  1
1980 Troll M, Dill KA, Zimm BH. Dynamics of polymer solutions. 3. An instrument for stress relaxations on dilute solutions of large polymer molecules Macromolecules. 13: 436-438. DOI: 10.1021/Ma60074A043  1
1980 Dill KA, Zimm BH. Dynamics of polymer solutions. 2. The determination of molecular weight distribution by viscoelasticity Macromolecules. 13: 432-436. DOI: 10.1021/Ma60074A042  1
1980 Dill KA, Zimm BH. Dynamics of polymer solutions. 1. Theory for an instrument Macromolecules. 13: 426-432. DOI: 10.1021/Ma60074A041  1
1979 Dill KA, Zimm BH. A rhelogical separator for very large DNA molecules. Nucleic Acids Research. 7: 735-49. PMID 388346 DOI: 10.1093/Nar/7.3.735  1
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