Ken Dill

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Chemicals & Drugs

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TOP 3
Druchok M; Vlachy V; Dill K A
Computer simulations of ionenes, hydrophobic ions with unusual solution thermodynamic properties. The ion-specific effects.
Fennell Christopher J; Bizjak Alan; Vlachy Vojko; Dill Ken A
Ion pairing in molecular simulations of aqueous alkali halide solutions.
Druchok M; Vlachy V; Dill K A
Explicit-water molecular dynamics study of a short-chain 3,3 ionene in solutions with sodium halides.

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All Publications

2009: Druchok M; Vlachy V; Dill K A
Computer simulations of ionenes, hydrophobic ions with unusual solution thermodynamic properties. The ion-specific effects.
The journal of physical chemistry. B 2009;113(43):14270-6.
2009: Fennell Christopher J; Bizjak Alan; Vlachy Vojko; Dill Ken A
Ion pairing in molecular simulations of aqueous alkali halide solutions.
The journal of physical chemistry. B 2009;113(19):6782-91.
2009: Druchok M; Vlachy V; Dill K A
Explicit-water molecular dynamics study of a short-chain 3,3 ionene in solutions with sodium halides.
The Journal of chemical physics 2009;130(13):134903.
2009: Shell M Scott; Ozkan S Banu; Voelz Vincent; Wu Guohong Albert; Dill Ken A
Blind test of physics-based prediction of protein structures.
Biophysical journal 2009;96(3):917-24.
2009: Ghosh Kingshuk; Dill K A
Theory for protein folding cooperativity: helix bundles.
Journal of the American Chemical Society 2009;131(6):2306-12.
2009: Watkins Gregory A; Jones Ella Fung; Scott Shell M; VanBrocklin Henry F; Pan Mei-Hsiu; Hanrahan Stephen M; Feng Jin Jin; He Jiang; Sounni Nor Eddine; Dill Ken A; Contag Christopher H; Coussens Lisa M; Franc Benjamin L
Development of an optimized activatable MMP-14 targeted SPECT imaging probe.
Bioorganic & medicinal chemistry 2009;17(2):653-9.
2009: MacCallum Justin L; Hua Lan; Schnieders Michael J; Pande Vijay S; Jacobson Matthew P; Dill Ken A
Assessment of the protein-structure refinement category in CASP8.
Proteins 2009;77 Suppl 9():66-80.
2008: Wu G Albert; Coutsias Evangelos A; Dill Ken A
Iterative assembly of helical proteins by optimal hydrophobic packing.
Structure (London, England : 1993) 2008;16(8):1257-66.
2008: Shell M Scott; Ritterson Ryan; Dill Ken A
A test on peptide stability of AMBER force fields with implicit solvation.
The journal of physical chemistry. B 2008;112(22):6878-86.
2008: Stock Gerhard; Ghosh Kingshuk; Dill Ken A
Maximum Caliber: a variational approach applied to two-state dynamics.
The Journal of chemical physics 2008;128(19):194102.
2008: Mobley David L; Barber Alan E; Fennell Christopher J; Dill Ken A
Charge asymmetries in hydration of polar solutes.
The journal of physical chemistry. B 2008;112(8):2405-14.
2008: Mobley David L; Dill Ken A; Chodera John D
Treating entropy and conformational changes in implicit solvent simulations of small molecules.
The journal of physical chemistry. B 2008;112(3):938-46.
2008: Dill Ken A; Ozkan S Banu; Shell M Scott; Weikl Thomas R
The protein folding problem.
Annual review of biophysics 2008;37():289-316.
2007: Urbic T; Vlachy V; Kalyuzhnyi Yu V; Dill K A
An improved thermodynamic perturbation theory for Mercedes-Benz water.
The Journal of chemical physics 2007;127(17):174511.
2007: Urbic T; Vlachy V; Kalyuzhnyi Yu V; Dill K A
Theory for the solvation of nonpolar solutes in water.
The Journal of chemical physics 2007;127(17):174505.
2007: Ghosh Kingshuk; Ozkan S Banu; Dill Ken A
The ultimate speed limit to protein folding is conformational searching.
Journal of the American Chemical Society 2007;129(39):11920-7.
2007: Mobley David L; Graves Alan P; Chodera John D; McReynolds Andrea C; Shoichet Brian K; Dill Ken A
Predicting absolute ligand binding free energies to a simple model site.
Journal of molecular biology 2007;371(4):1118-34.
2007: Ozkan S Banu; Wu G Albert; Chodera John D; Dill Ken A
Protein folding by zipping and assembly.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(29):11987-92.
2007: Dill Ken A; Ozkan S Banu; Weikl Thomas R; Chodera John D; Voelz Vincent A
The protein folding problem: when will it be solved?
Current opinion in structural biology 2007;17(3):342-6.
2007: Bradford Justin A; Dill Ken A
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 2007;104(24):10098-103.
2007: Chodera John D; Singhal Nina; Pande Vijay S; Dill Ken A; Swope William C
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.
The Journal of chemical physics 2007;126(15):155101.
2007: Lucas Adam; Huang Liang; Joshi Aravind; Dill Ken A
Statistical mechanics of helix bundles using a dynamic programming approach.
Journal of the American Chemical Society 2007;129(14):4272-81.
2007: Seitaridou Effrosyni; Inamdar Mandar M; Phillips Rob; Ghosh Kingshuk; Dill Ken
Measuring flux distributions for diffusion in the small-numbers limit.
The journal of physical chemistry. B 2007;111(9):2288-92.
2007: Mobley David L; Dumont Elise; Chodera John D; Dill Ken A
Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.
The journal of physical chemistry. B 2007;111(9):2242-54.
2007: Voelz Vincent A; Dill Ken A
Exploring zipping and assembly as a protein folding principle.
Proteins 2007;66(4):877-88.
2007: Weikl Thomas R; Dill Ken A
Transition-states in protein folding kinetics: the structural interpretation of Phi values.
Journal of molecular biology 2007;365(5):1578-86.
2007: Hockenmaier Julia; Joshi Aravind K; Dill Ken A
Routes are trees: the parsing perspective on protein folding.
Proteins 2007;66(1):1-15.
2006: Mobley David L; Chodera John D; Dill Ken A
On the use of orientational restraints and symmetry corrections in alchemical free energy calculations.
The Journal of chemical physics 2006;125(8):084902.
2006: Ho Bosco K; Dill Ken A
Folding very short peptides using molecular dynamics.
PLoS computational biology 2006;2(4):e27.
2006: Urbic T; Vlachy V; Dill K A
Confined water: a Mercedes-Benz model study.
The journal of physical chemistry. B 2006;110(10):4963-70.
2006: Chiang David; Joshi Aravind K; Dill Ken A
A grammatical theory for the conformational changes of simple helix bundles.
Journal of computational biology : a journal of computational molecular cell biology 2006;13(1):21-42.
2005: Chorny Ilya; Dill Ken A; Jacobson Matthew P
Surfaces affect ion pairing.
The journal of physical chemistry. B 2005;109(50):24056-60.
2005: Xu Huafeng; Dill Ken A
Water's hydrogen bonds in the hydrophobic effect: a simple model.
The journal of physical chemistry. B 2005;109(49):23611-7.
2005: Coutsias Evangelos A; Seok Chaok; Dill Ken A
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 2005;26(15):1663-5.
2005: Lee Byoung-Chul; Zuckermann Ronald N; Dill Ken A
Folding a nonbiological polymer into a compact multihelical structure.
Journal of the American Chemical Society 2005;127(31):10999-1009.
2005: Merlo Claudia; Dill Ken A; Weikl Thomas R
Phi values in protein-folding kinetics have energetic and structural components.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(29):10171-5.
2005: Ho Bosco K; Coutsias Evangelos A; Seok Chaok; Dill Ken A
The flexibility in the proline ring couples to the protein backbone.
Protein science : a publication of the Protein Society 2005;14(4):1011-8.
2005: Jaswal Sheila S; Truhlar Stephanie M E; Dill Ken A; Agard David A
Comprehensive analysis of protein folding activation thermodynamics reveals a universal behavior violated by kinetically stable proteases.
Journal of molecular biology 2005;347(2):355-66.
2005: Dill Ken A; Truskett Thomas M; Vlachy Vojko; Hribar-Lee Barbara
Modeling water, the hydrophobic effect, and ion solvation.
Annual review of biophysics and biomolecular structure 2005;34():173-99.
2004: Coutsias Evangelos A; Seok Chaok; Dill Ken A
Using quaternions to calculate RMSD.
Journal of computational chemistry 2004;25(15):1849-57.
2004: Horn Thomas; Lee Byoung-Chul; Dill Ken A; Zuckermann Ronald N
Incorporation of chemoselective functionalities into peptoids via solid-phase submonomer synthesis.
Bioconjugate chemistry 2004;15(2):428-35.
2004: Weikl Thomas R; Palassini Matteo; Dill Ken A
Cooperativity in two-state protein folding kinetics.
Protein science : a publication of the Protein Society 2004;13(3):822-9.
2004: Coutsias Evangelos A; Seok Chaok; Jacobson Matthew P; Dill Ken A
A kinematic view of loop closure.
Journal of computational chemistry 2004;25(4):510-28.
2003: Wu Cindy W; Kirshenbaum Kent; Sanborn Tracy J; Patch James A; Huang Kai; Dill Ken A; Zuckermann Ronald N; Barron Annelise E
Structural and spectroscopic studies of peptoid oligomers with alpha-chiral aliphatic side chains.
Journal of the American Chemical Society 2003;125(44):13525-30.
2003: Schonbrun Jack; Dill Ken A
Fast protein folding kinetics.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(22):12678-82.
2003: Truskett Thomas M; Dill Ken A
A simple analytical model of water.
Biophysical chemistry 2003;105(2-3):449-59.
2003: Weikl Thomas R; Dill Ken A
Folding kinetics of two-state proteins: effect of circularization, permutation, and crosslinks.
Journal of molecular biology 2003;332(4):953-63.
2003: Weikl Thomas R; Dill Ken A
Folding rates and low-entropy-loss routes of two-state proteins.
Journal of molecular biology 2003;329(3):585-98.
2003: Ozkan S Banu; Dill Ken A; Bahar Ivet
Computing the transition state populations in simple protein models.
Biopolymers 2003;68(1):35-46.
2003: Seok Chaok; Rosen J B; Chodera John D; Dill Ken A
MOPED: method for optimizing physical energy parameters using decoys.
Journal of computational chemistry 2003;24(1):89-97.
2003: Amato Nancy M; Dill Ken A; Song Guang
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 2003;10(3-4):239-55.
2003: Song Guang; Thomas Shawna; Dill Ken A; Scholtz J Martin; Amato Nancy M
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 2003;():240-51.
2002: Southall Noel T; Dill Ken A
Potential of mean force between two hydrophobic solutes in water.
Biophysical chemistry 2002;101-102():295-307.
2002: Hribar Barbara; Southall Noel T; Vlachy Vojko; Dill Ken A
How ions affect the structure of water.
Journal of the American Chemical Society 2002;124(41):12302-11.
2002: Ozkan S Banu; Dill Ken A; Bahar Ivet
Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model.
Protein science : a publication of the Protein Society 2002;11(8):1958-70.
2002: Ball Keith D; Erman Burak; Dill Ken A
The elastic net algorithm and protein structure prediction.
Journal of computational chemistry 2002;23(1):77-83.
2001: Zhou H X; Dill K A
Stabilization of proteins in confined spaces.
Biochemistry 2001;40(38):11289-93.
2001: Ozkan S B; Bahar I; Dill K A
Transition states and the meaning of Phi-values in protein folding kinetics.
Nature structural biology 2001;8(9):765-9.
2001: Liang J; Dill K A
Are proteins well-packed?
Biophysical journal 2001;81(2):751-66.
2000: Rosen J B; Phillips A T; Oh S Y; Dill K A
A method for parameter optimization in computational biology.
Biophysical journal 2000;79(6):2818-24.
2000: Yue K; Dill K A
Constraint-based assembly of tertiary protein structures from secondary structure elements.
Protein science : a publication of the Protein Society 2000;9(10):1935-46.
2000: Chen S J; Dill K A
RNA folding energy landscapes.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(2):646-51.
1999: Young M; Kirshenbaum K; Dill K A; Highsmith S
Predicting conformational switches in proteins.
Protein science : a publication of the Protein Society 1999;8(9):1752-64.
1999: Kirshenbaum K; Zuckermann R N; Dill K A
Designing polymers that mimic biomolecules.
Current opinion in structural biology 1999;9(4):530-5.
1999: Dill K A
Strengthening biomedicine's roots.
Nature 1999;400(6742):309-10.
1999: Dill K A
Polymer principles and protein folding.
Protein science : a publication of the Protein Society 1999;8(6):1166-80.
1999: Brem R; Dill K A
The effect of multiple binding modes on empirical modeling of ligand docking to proteins.
Protein science : a publication of the Protein Society 1999;8(5):1134-43.
1999: Ishikawa K; Yue K; Dill K A
Predicting the structures of 18 peptides using Geocore.
Protein science : a publication of the Protein Society 1999;8(4):716-21.
1998: Tang K E; Dill K A
Native protein fluctuations: the conformational-motion temperature and the inverse correlation of protein flexibility with protein stability.
Journal of biomolecular structure & dynamics 1998;16(2):397-411.
1998: Armand P; Kirshenbaum K; Goldsmith R A; Farr-Jones S; Barron A E; Truong K T; Dill K A; Mierke D F; Cohen F E; Zuckermann R N; Bradley E K
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 1998;95(8):4309-14.
1998: Kirshenbaum K; Barron A E; Goldsmith R A; Armand P; Bradley E K; Truong K T; Dill K A; Cohen F E; Zuckermann R N
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 1998;95(8):4303-8.
1998: Chan H S; Dill K A
Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics.
Proteins 1998;30(1):2-33.
1997: Miller D W; Dill K A
Ligand binding to proteins: the binding landscape model.
Protein science : a publication of the Protein Society 1997;6(10):2166-79.
1997: Dill K A
Additivity principles in biochemistry.
The Journal of biological chemistry 1997;272(2):701-4.
1997: Dill K A; Chan H S
From Levinthal to pathways to funnels.
Nature structural biology 1997;4(1):10-9.
1997: Armand P; Kirshenbaum K; Falicov A; Dunbrack R L; Dill K A; Zuckermann R N; Cohen F E
Chiral N-substituted glycines can form stable helical conformations.
Folding & design 1997;2(6):369-75.
1997: Dill K A; Phillips A T; Rosen J B
Protein structure and energy landscape dependence on sequence using a continuous energy function.
Journal of computational biology : a journal of computational molecular cell biology 1997;4(3):227-39.
1997: Chan H S; Dill K A
Solvation: how to obtain microscopic energies from partitioning and solvation experiments.
Annual review of biophysics and biomolecular structure 1997;26():425-59.
1996: Beutler T C; Dill K A
A fast conformational search strategy for finding low energy structures of model proteins.
Protein science : a publication of the Protein Society 1996;5(10):2037-43.
1996: Stigter D; Dill K A
Binding of ionic ligands to polyelectrolytes.
Biophysical journal 1996;71(4):2064-74.
1996: Thomas P D; Dill K A
An iterative method for extracting energy-like quantities from protein structures.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(21):11628-33.
1996: Chan H S; Dill K A
A simple model of chaperonin-mediated protein folding.
Proteins 1996;24(3):345-51.
1996: Chan H S; Dill K A
Comparing folding codes for proteins and polymers.
Proteins 1996;24(3):335-44.
1996: Thomas P D; Dill K A
Statistical potentials extracted from protein structures: how accurate are they?
Journal of molecular biology 1996;257(2):457-69.
1996: Yue K; Dill K A
Folding proteins with a simple energy function and extensive conformational searching.
Protein science : a publication of the Protein Society 1996;5(2):254-61.
1995: Sun S; Brem R; Chan H S; Dill K A
Designing amino acid sequences to fold with good hydrophobic cores.
Protein engineering 1995;8(12):1205-13.
1995: Miller D W; Dill K A
A statistical mechanical model for hydrogen exchange in globular proteins.
Protein science : a publication of the Protein Society 1995;4(9):1860-73.
1995: Sun S; Thomas P D; Dill K A
A simple protein folding algorithm using a binary code and secondary structure constraints.
Protein engineering 1995;8(8):769-78.
1995: Chan H S; Bromberg S; Dill K A
Models of cooperativity in protein folding.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences 1995;348(1323):61-70.
1995: Dill K A; Bromberg S; Yue K; Fiebig K M; Yee D P; Thomas P D; Chan H S
Principles of protein folding--a perspective from simple exact models.
Protein science : a publication of the Protein Society 1995;4(4):561-602.
1995: Yue K; Fiebig K M; Thomas P D; Chan H S; Shakhnovich E I; Dill K A
A test of lattice protein folding algorithms.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(1):325-9.
1995: Yue K; Dill K A
Forces of tertiary structural organization in globular proteins.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(1):146-50.
1995: Dill K A; Stigter D
Modeling protein stability as heteropolymer collapse.
Advances in protein chemistry 1995;46():59-104.
1994: Yee D P; Chan H S; Havel T F; Dill K A
Does compactness induce secondary structure in proteins? A study of poly-alanine chains computed by distance geometry.
Journal of molecular biology 1994;241(4):557-73.
1994: Bromberg S; Dill K A
Side-chain entropy and packing in proteins.
Protein science : a publication of the Protein Society 1994;3(7):997-1009.
1994: Lattman E E; Fiebig K M; Dill K A
Modeling compact denatured states of proteins.
Biochemistry 1994;33(20):6158-66.
1993: Thomas P D; Dill K A
Local and nonlocal interactions in globular proteins and mechanisms of alcohol denaturation.
Protein science : a publication of the Protein Society 1993;2(12):2050-65.
1993: Yee D P; Dill K A
Families and the structural relatedness among globular proteins.
Protein science : a publication of the Protein Society 1993;2(6):884-99.
1993: De Young L R; Dill K A; Fink A L
Aggregation and denaturation of apomyoglobin in aqueous urea solutions.
Biochemistry 1993;32(15):3877-86.
1993: Dill K A; Fiebig K M; Chan H S
Cooperativity in protein-folding kinetics.
Proceedings of the National Academy of Sciences of the United States of America 1993;90(5):1942-6.
1992: Stickle D F; Presta L G; Dill K A; Rose G D
Hydrogen bonding in globular proteins.
Journal of molecular biology 1992;226(4):1143-59.
1992: Cole L A; Dorsey J G; Dill K A
Temperature dependence of retention in reversed-phase liquid chromatography. 2. Mobile-phase considerations.
Analytical chemistry 1992;64(13):1324-7.
1992: Stigter D; Mingins J; Dill K A
Phospholipid interactions in model membrane systems. II. Theory.
Biophysical journal 1992;61(6):1616-29.
1992: Mingins J; Stigter D; Dill K A
Phospholipid interactions in model membrane systems. I. Experiments on monolayers.
Biophysical journal 1992;61(6):1603-15.
1992: Yue K; Dill K A
Inverse protein folding problem: designing polymer sequences.
Proceedings of the National Academy of Sciences of the United States of America 1992;89(9):4163-7.
1992: Shortle D; Chan H S; Dill K A
Modeling the effects of mutations on the denatured states of proteins.
Protein science : a publication of the Protein Society 1992;1(2):201-15.
1991: Alonso D O; Dill K A; Stigter D
The three states of globular proteins: acid denaturation.
Biopolymers 1991;31(13):1631-49.
1991: Alonso D O; Dill K A
Solvent denaturation and stabilization of globular proteins.
Biochemistry 1991;30(24):5974-85.
1991: Kollman P A; Dill K A
Decisions in force field development: an alternative to those described by Roterman et al. (J. Biomol. Struct. Dyn. 7, 421 (1989)).
Journal of biomolecular structure & dynamics 1991;8(6):1103-7; discussion 1109-11.
1991: Stigter D; Alonso D O; Dill K A
Protein stability: electrostatics and compact denatured states.
Proceedings of the National Academy of Sciences of the United States of America 1991;88(10):4176-80.
1991: Dill K A; Shortle D
Denatured states of proteins.
Annual review of biochemistry 1991;60():795-825.
1991: Chan H S; Dill K A
Polymer principles in protein structure and stability.
Annual review of biophysics and biophysical chemistry 1991;20():447-90.
1990: Dill K A
The meaning of hydrophobicity.
Science (New York, N.Y.) 1990;250(4978):297-8.
1990: Chan H S; Dill K A
Origins of structure in globular proteins.
Proceedings of the National Academy of Sciences of the United States of America 1990;87(16):6388-92.
1990: Dill K A
Dominant forces in protein folding.
Biochemistry 1990;29(31):7133-55.
1990: Stigter D; Dill K A
Charge effects on folded and unfolded proteins.
Biochemistry 1990;29(5):1262-71.
1990: Lau K F; Dill K A
Theory for protein mutability and biogenesis.
Proceedings of the National Academy of Sciences of the United States of America 1990;87(2):638-42.
1989: Ying P T; Dorsey J G; Dill K A
Retention mechanisms of reversed-phase liquid chromatography: determination of solute-solvent interaction free energies.
Analytical chemistry 1989;61(22):2540-6.
1989: Dill K A; Alonso D O; Hutchinson K
Thermal stabilities of globular proteins.
Biochemistry 1989;28(13):5439-49.
1988: De Young L R; Dill K A
Solute partitioning into lipid bilayer membranes.
Biochemistry 1988;27(14):5281-9.
1988: Dill K A; Stigter D
Lateral interactions among phosphatidylcholine and phosphatidylethanolamine head groups in phospholipid monolayers and bilayers.
Biochemistry 1988;27(9):3446-53.
1988: Dill K A; Naghizadeh J; Marqusee J A
Chain molecules at high densities at interfaces.
Annual review of physical chemistry 1988;39():425-61.
1987: Dill K A
Protein surgery.
Protein engineering 1987;1(5):369-71.
1986: Dill K A
The chain conformations in membranes and micelles.
Advances in colloid and interface science 1986;26(2-4):99-110.
1985: Dill K A
Theory for the folding and stability of globular proteins.
Biochemistry 1985;24(6):1501-9.
1981: Tullis R H; Dill K A; Price P A
Fluorescence and kinetic studies on the divalent metal ion induced conformational changes in DNase a.
The Journal of biological chemistry 1981;256(11):5656-61.
1979: Dill K A; Zimm B H
A rhelogical separator for very large DNA molecules.
Nucleic acids research 1979;7(3):735-49.

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