Ken A. Dill

Q: What Schools Are Affiliated With Ken A. Dill

Ken A. Dill is affiliated with the following schools: University of California, San Francisco, Columbia University, University of New Orleans, Seoul National University, Technical University of Denmark, University of Ljubljana, University of California, Berkeley, Stony Brook University, University of Sydney, University of Houston, University of California, San Diego, Massachusetts Institute of Technology

Ken A. Dill's AcademicInfluence.com Rankings

Ken A. Dill

Chemistry

#776

World Rank

#1293

Historical Rank

#333

USA Rank

chemistry Degrees

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Chemistry

Ken A. Dill's Degrees

PhD Chemistry University of California, Berkeley
Bachelors Chemistry University of California, Berkeley

Why Is Ken A. Dill Influential?

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According to Wikipedia, Kenneth Austin Dill is a biophysicist and chemist best known for his work in folding pathways of proteins. He is the director of the Louis and Beatrice Laufer Center for Physical and Quantitative Biology at Stony Brook University. He was elected a member of the National Academy of Sciences in 2008. He was elected to the American Academy of Arts and Sciences in 2014. He has been a co-editor or editor of the Annual Review of Biophysics since 2013.

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Ken A. Dill's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

Dominant forces in protein folding. (1990) (3315)
From Levinthal to pathways to funnels (1997) (2213)
Principles of protein folding — A perspective from simple exact models (1995) (1399)
Theory for the folding and stability of globular proteins. (1985) (1184)
The Protein-Folding Problem, 50 Years On (2012) (1176)
The protein folding problem. (1993) (1157)
A lattice statistical mechanics model of the conformational and sequence spaces of proteins (1989) (887)
Denatured states of proteins. (1991) (837)
A View of the Hydrophobic Effect (2002) (671)
How ions affect the structure of water. (2002) (587)
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. (2007) (559)
Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". (2009) (481)
Cooperativity in protein-folding kinetics. (1993) (435)
Protein folding in the landscape perspective: Chevron plots and non‐arrhenius kinetics (1998) (423)
Statistical potentials extracted from protein structures: how accurate are they? (1996) (420)
Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations. (2007) (414)
Polymer principles and protein folding (1999) (396)
Sequence-specific polypeptoids: a diverse family of heteropolymers with stable secondary structure. (1998) (350)
Stabilization of proteins in confined spaces. (2001) (348)
Molecular driving forces : statistical thermodynamics in chemistry and biology (2002) (347)
The molecular mechanism of retention in reversed-phase liquid chromatography (1989) (340)
Modeling water, the hydrophobic effect, and ion solvation. (2005) (333)
Using quaternions to calculate RMSD (2004) (321)
Additivity Principles in Biochemistry* (1997) (319)
Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations. (2009) (315)
Hydrogen bonding in globular proteins. (1992) (315)
Principles of maximum entropy and maximum caliber in statistical physics (2013) (311)
Origins of structure in globular proteins. (1990) (296)
A test of lattice protein folding algorithms. (1995) (283)
Polymer principles in protein structure and stability. (1991) (273)
Transition states and folding dynamics of proteins and heteropolymers (1994) (270)
Predicting absolute ligand binding free energies to a simple model site. (2007) (265)
Molecular driving forces (2002) (261)
A kinematic view of loop closure (2004) (260)
Ion pairing in molecular simulations of aqueous alkali halide solutions. (2009) (255)
The protein folding problem: when will it be solved? (2007) (248)
Physical limits of cells and proteomes (2011) (247)
On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. (2006) (246)
A Simple Model of Water and the Hydrophobic Effect (1998) (245)
Are proteins well-packed? (2001) (241)
Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. (2007) (236)
An iterative method for extracting energy-like quantities from protein structures. (1996) (227)
Local and nonlocal interactions in globular proteins and mechanisms of alcohol denaturation (1993) (224)
Theory for protein mutability and biogenesis. (1990) (221)
The mechanism of solute retention in reversed-phase liquid chromatography (1987) (220)
NMR determination of the major solution conformation of a peptoid pentamer with chiral side chains. (1998) (219)
Solvent denaturation and stabilization of globular proteins. (1991) (214)
How Water’s Properties Are Encoded in Its Molecular Structure and Energies (2017) (214)
Structural and Spectroscopic Studies of Peptoid Oligomers with α-Chiral Aliphatic Side Chains (2003) (207)
Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations (2006) (206)
Solute partitioning into lipid bilayer membranes. (1988) (206)
Molecular driving forces : statistical thermodynamics in biology, chemistry, physics, and nanoscience (2012) (198)
Thermal stabilities of globular proteins. (1989) (192)
RNA folding energy landscapes. (2000) (188)
The effects of internal constraints on the configurations of chain molecules (1990) (181)
Forces of tertiary structural organization in globular proteins. (1995) (178)
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. (2013) (175)
The meaning of hydrophobicity. (1990) (168)
Intrachain loops in polymers: Effects of excluded volume (1989) (168)
Inverse protein folding problem: designing polymer sequences. (1992) (166)
‘‘Sequence space soup’’ of proteins and copolymers (1991) (166)
In silico selection of therapeutic antibodies for development: Viscosity, clearance, and chemical stability (2014) (165)
Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. (2009) (159)
The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change. (2007) (156)
Designing polymers that mimic biomolecules. (1999) (150)
Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures (2002) (148)
Biomimetic nanostructures: creating a high-affinity zinc-binding site in a folded nonbiological polymer. (2008) (148)
Ligand binding to proteins: The binding landscape model (1997) (146)
Protein folding by zipping and assembly (2007) (143)
The interphase in lamellar semicrystalline polymers (1984) (141)
Why Do Fast-Growing Bacteria Enter Overflow Metabolism? Testing the Membrane Real Estate Hypothesis. (2017) (139)
Partitioning of nonpolar solutes into bilayers and amorphous n-alkanes (1990) (138)
The Mechanism of Hydrophobic Solvation Depends on Solute Radius (2000) (136)
Native protein fluctuations: the conformational-motion temperature and the inverse correlation of protein flexibility with protein stability. (1998) (136)
Transition states and the meaning of Φ-values in protein folding kinetics (2001) (136)
Chiral N-substituted glycines can form stable helical conformations. (1997) (134)
Aggregation of globular proteins (1993) (134)
Side‐chain entropy and packing in proteins (1994) (132)
Protein stability: electrostatics and compact denatured states. (1991) (132)
Bacterial growth laws reflect the evolutionary importance of energy efficiency (2014) (132)
Solute partitioning into chain molecule interphases: Monolayers, bilayer membranes, and micelles (1986) (126)
A test on peptide stability of AMBER force fields with implicit solvation. (2008) (123)
The Strength of Hydrogen Bonds in Liquid Water and Around Nonpolar Solutes (2000) (118)
What drives amyloid molecules to assemble into oligomers and fibrils? (2010) (116)
Modeling the effects of mutations on the denatured states of proteins (1992) (115)
A simple protein folding algorithm using a binary code and secondary structure constraints. (1995) (114)
Protein core assembly processes (1993) (114)
Aggregation and denaturation of apomyoglobin in aqueous urea solutions. (1993) (113)
Folding a nonbiological polymer into a compact multihelical structure. (2005) (113)
Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference (2015) (112)
Advances in free-energy-based simulations of protein folding and ligand binding. (2016) (107)
A fast conformational search strategy for finding low energy structures of model proteins (1996) (106)
Energy landscapes and the collapse dynamics of homopolymers (1993) (103)
Designing amino acid sequences to fold with good hydrophobic cores. (1995) (102)
Treating entropy and conformational changes in implicit solvent simulations of small molecules. (2008) (101)
Nonuniversal power law scaling in the probability distribution of scientific citations (2010) (100)
Modeling protein stability as heteropolymer collapse. (1995) (99)
Folding kinetics of proteins and copolymers (1992) (99)
Cellular proteomes have broad distributions of protein stability. (2010) (98)
Assessment of protein structure refinement in CASP9 (2011) (96)
Computing protein stabilities from their chain lengths (2009) (95)
Models of cooperativity in protein folding. (1995) (94)
Modeling compact denatured states of proteins. (1994) (93)
Theory for the aggregation of proteins and copolymers (1992) (93)
Comparing folding codes for proteins and polymers (1996) (91)
Charge effects on folded and unfolded proteins. (1990) (91)
Charge asymmetries in hydration of polar solutes. (2008) (91)
Molecular conformations in surfactant micelles (1984) (91)
Predictions of hydration free energies from all-atom molecular dynamics simulations. (2009) (88)
Conformations and Forces in Protein Folding (1991) (86)
Folding Very Short Peptides Using Molecular Dynamics (2006) (86)
Molecular model of hydrophobic solvation (1999) (86)
Annual review of biophysics (2008) (86)
Folding rates and low-entropy-loss routes of two-state proteins. (2003) (85)
Folding proteins: finding a needle in a haystack (1993) (83)
A statistical mechanical model for hydrogen exchange in globular proteins (1995) (83)
Protein aggregation in salt solutions (2015) (82)
Predicting conformational switches in proteins (1999) (81)
Folding proteins with a simple energy function and extensive conformational searching (1996) (80)
A simple model of chaperonin‐mediated protein folding (1996) (79)
De novo structure prediction and experimental characterization of folded peptoid oligomers (2012) (77)
Accelerating molecular simulations of proteins using Bayesian inference on weak information (2015) (76)
Proteostasis collapse is a driver of cell aging and death (2019) (76)
Fast protein folding kinetics (2003) (75)
Assessment of the protein‐structure refinement category in CASP8 (2009) (74)
The ultimate speed limit to protein folding is conformational searching. (2007) (73)
Families and the structural relatedness among globular proteins (1993) (72)
Chain molecules at high densities at interfaces. (1988) (71)
Temperature dependence of retention in reversed-phase liquid chromatography. 2. Mobile-phase considerations. (1992) (70)
Fast‐folding protein kinetics, hidden intermediates, and the sequential stabilization model (2002) (70)
The flexibility in the proline ring couples to the protein backbone (2005) (69)
Perspective: Maximum caliber is a general variational principle for dynamical systems. (2017) (68)
Solvation: how to obtain microscopic energies from partitioning and solvation experiments. (1997) (67)
Cooperativity in two‐state protein folding kinetics (2003) (66)
ChemInform Abstract: A View of the Hydrophobic Effect (2002) (66)
Does compactness induce secondary structure in proteins? A study of poly-alanine chains computed by distance geometry. (1994) (66)
Modeling aqueous solvation with semi-explicit assembly (2011) (65)
The three states of globular proteins: Acid denaturation (1991) (64)
Lateral interactions among phosphatidylcholine and phosphatidylethanolamine head groups in phospholipid monolayers and bilayers. (1988) (63)
Simple liquid models with corrected dielectric constants. (2012) (63)
Frequency dependence of NMR spin lattice relaxation in bilayer membranes (1984) (62)
Theory for protein folding cooperativity: helix bundles. (2009) (61)
Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations. (2015) (60)
Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes. (2015) (59)
Development of an optimized activatable MMP-14 targeted SPECT imaging probe. (2009) (59)
Diet modulates brain network stability, a biomarker for brain aging, in young adults (2020) (58)
Resultants and Loop Closure (2006) (58)
Blind protein structure prediction using accelerated free-energy simulations (2016) (56)
Maximum Caliber: a variational approach applied to two-state dynamics. (2008) (56)
Computed Binding of Peptides to Proteins with MELD-Accelerated Molecular Dynamics. (2017) (55)
A two-dimensional model of water: Theory and computer simulations (2000) (55)
General mechanism of two-state protein folding kinetics. (2014) (55)
Nonadditive entropies yield probability distributions with biases not warranted by the data. (2013) (54)
Highly Charged Proteins: The Achilles' Heel of Aging Proteomes. (2016) (53)
Surface-induced enhancement of internal structure in polymers and proteins (1990) (52)
Molecular Motors: Power Strokes Outperform Brownian Ratchets. (2016) (52)
Folding kinetics of two-state proteins: effect of circularization, permutation, and crosslinks. (2003) (52)
Potential of mean force between two hydrophobic solutes in water. (2002) (52)
Blind prediction of charged ligand binding affinities in a model binding site. (2013) (51)
A Simple Statistical Mechanical Model of Water (2002) (50)
Teaching the principles of statistical dynamics. (2005) (50)
A two-dimensional model of water: Solvation of nonpolar solutes (2002) (49)
Solvation: Effects of molecular size and shape (1994) (49)
Protein Structure and Energy Landscape Dependence on Sequence Using a Continuous Energy Function (1997) (49)
Bacterial proteostasis balances energy and chaperone utilization efficiently (2017) (49)
Orientation-dependent integral equation theory for a two-dimensional model of water (2003) (48)
Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER. (2011) (47)
Oil/water transfer is partly driven by molecular shape, not just size. (2010) (45)
Computing the transition state populations in simple protein models. (2003) (45)
Blind test of physics-based prediction of protein structures. (2009) (45)
Theory for the three-dimensional Mercedes-Benz model of water. (2009) (44)
Statistical thermodynamics of double‐stranded polymer molecules (1995) (44)
Oil/Water Partitioning Has a Different Thermodynamic Signature When the Oil Solvent Chains Are Aligned Than When They Are Amorphous (1998) (44)
Protein evolution speed depends on its stability and abundance and on chaperone concentrations (2018) (44)
Surfaces affect ion pairing. (2005) (43)
Phi values in protein-folding kinetics have energetic and structural components. (2005) (42)
Comprehensive analysis of protein folding activation thermodynamics reveals a universal behavior violated by kinetically stable proteases. (2005) (42)
The Maximum Caliber Variational Principle for Nonequilibria. (2020) (41)
Water's hydrogen bonds in the hydrophobic effect: a simple model. (2005) (41)
Predicting water’s phase diagram and liquid-state anomalies (2002) (41)
Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge (2021) (40)
Theory for the conformational changes of double-stranded chain molecules (1998) (40)
Binding of ionic ligands to polyelectrolytes. (1996) (39)
A Path Planning-Based Study of Protein Folding with a Case Study of Hairpin Formation in Protein G and L (2002) (38)
Molecular Simulations Identify Binding Poses and Approximate Affinities of Stapled α-Helical Peptides to MDM2 and MDMX. (2017) (38)
Physical Modeling of Aqueous Solvation (2011) (38)
Retention mechanisms of reversed-phase liquid chromatography: determination of solute-solvent interaction free energies. (1989) (37)
Symmetry and designability for lattice protein models (2000) (37)
Hydrophobicity in a simple model of water: Entropy penalty as a sum of competing terms via full, angular expansion (2001) (37)
Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers (2017) (37)
Structural and spectroscopic studies of peptoid oligomers with alpha-chiral aliphatic side chains. (2003) (37)
Strengthening biomedicine's roots (1999) (36)
Routes are trees: The parsing perspective on protein folding (2006) (36)
Incorporation of chemoselective functionalities into peptoids via solid-phase submonomer synthesis. (2004) (36)
Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments (2009) (36)
Protein storytelling through physics (2020) (36)
Markov processes follow from the principle of maximum caliber. (2011) (35)
A maximum entropy framework for nonexponential distributions (2013) (35)
Confined water: a Mercedes-Benz model study. (2006) (34)
Transition-states in protein folding kinetics: the structural interpretation of Phi values. (2006) (34)
Enhanced structure in polymers at interfaces (1991) (33)
Phospholipid interactions in model membrane systems. I. Experiments on monolayers. (1992) (33)
Controlling the viscosities of antibody solutions through control of their binding sites. (2017) (32)
Growth rates of protein crystals. (2012) (32)
Water-like fluid in the presence of Lennard–Jones obstacles: predictions of an associative replica Ornstein–Zernike theory☆ (2004) (31)
Phospholipid interactions in model membrane systems. II. Theory. (1992) (31)
Modeling stochastic dynamics in biochemical systems with feedback using maximum caliber. (2011) (30)
Exploring zipping and assembly as a protein folding principle (2006) (30)
Statistical thermodynamics of short-chain molecule interphases. 1. Theory (1984) (30)
Measuring flux distributions for diffusion in the small-numbers limit. (2007) (29)
Extracting conformational memory from single-molecule kinetic data. (2013) (29)
Mechanisms for achieving high speed and efficiency in biomolecular machines (2019) (29)
A tabu search strategy for finding low energy structures of proteins in HP - model (2004) (29)
Inferring Microscopic Kinetic Rates from Stationary State Distributions (2014) (28)
Constraint-based assembly of tertiary protein structures from secondary structure elements. (2000) (28)
Field-SEA: A Model for Computing the Solvation Free Energies of Nonpolar, Polar, and Charged Solutes in Water (2013) (28)
Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations (2013) (27)
Theory for the solvation of nonpolar solutes in water. (2007) (27)
Aqueous alkali halide solutions: can osmotic coefficients be explained on the basis of the ionic sizes alone? (2010) (27)
An improved thermodynamic perturbation theory for Mercedes-Benz water. (2007) (27)
Chain configurations in lamellar semicrystalline polymer interphases (1986) (27)
Biophysics. Introduction. (2013) (26)
Calculating the sensitivity and robustness of binding free energy calculations to force field parameters. (2013) (26)
How Do Chaperones Protect a Cell's Proteins from Oxidative Damage? (2018) (25)
Trajectory approach to two-state kinetics of single particles on sculpted energy landscapes. (2008) (25)
Decisions in force field development: an alternative to those described by Roterman et al. (J. Biomol. Struct. Dyn. 7, 421 (1989)). (1991) (25)
Computing the relative stabilities and the per-residue components in protein conformational changes. (2014) (25)
Single Molecule Conformational Memory Extraction: P5ab RNA Hairpin (2014) (25)
Predicting the structures of 18 peptides using Geocore (2008) (25)
Theory for the separation of very large DNA molecules by radial migration. (1979) (25)
Hydrophobicity reinterpreted as ‘minimisation of the entropy penalty of solvation’ (1996) (25)
FlexE: Using elastic network models to compare models of protein structure. (2012) (25)
Protein Actions: Principles and Modeling (2017) (25)
Separated topologies--a method for relative binding free energy calculations using orientational restraints. (2013) (25)
Free energy of electrical double layers: entropy of adsorbed ions and the binding polynomial (1989) (24)
CGU: An Algorithm for Molecular Structure Prediction (1997) (24)
The protein folding problem: The role of theory. (2021) (24)
Gaussian model of protein folding (2000) (24)
Caliber Corrected Markov Modeling (C2M2): Correcting Equilibrium Markov Models. (2017) (24)
Lateral interactions among phospholipid head groups at the heptane/water interface (1988) (24)
Configurations of the amphiphilic molecules in micelles (1982) (23)
Role of Proteome Physical Chemistry in Cell Behavior (2016) (22)
Reply to C. Tsallis' "Conceptual Inadequacy of the Shore and Johnson Axioms for Wide Classes of Complex Systems" (2015) (22)
Water Is a Cagey Liquid. (2018) (22)
A statistical mechanical theory for a two-dimensional model of water. (2010) (22)
Comparing search strategies for finding global optima on energy landscapes (1999) (22)
The elastic net algorithm and protein structure prediction (2002) (22)
Communication: Maximum caliber is a general variational principle for nonequilibrium statistical mechanics. (2015) (22)
Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test (2012) (21)
Theory for second virial coefficients of short DNA (1993) (21)
Molecular Structure Prediction by Global Optimization (1997) (21)
MOPED: Method for optimizing physical energy parameters using decoys (2003) (20)
Theory for protein solubilities (1993) (19)
Theory for the Equation of State of Phospholipid Monolayers (1986) (19)
Using Interpolation for Fast and Accurate Calculation of Ion–Ion Interactions (2014) (19)
A simple analytical model of water. (2003) (19)
Electrostatics and aggregation: how charge can turn a crystal into a gel. (2010) (19)
Dynamical fluctuations in biochemical reactions and cycles. (2010) (18)
Simulated Evolution of Protein-Protein Interaction Networks with Realistic Topology (2012) (17)
NMR‐assisted protein structure prediction with MELDxMD (2019) (16)
Simple model of hydrophobic hydration. (2012) (16)
Symmetries in proteins: A knot theory approach (1996) (16)
Statistical mechanics of pseudoknot polymers (2003) (16)
Statistical thermodynamics of short chain molecule interphases. 2. Configurational properties of amphiphilic aggregates (1984) (15)
The stabilities of protein crystals. (2010) (15)
Accelerating physical simulations of proteins by leveraging external knowledge (2017) (15)
Receptacle model of salting-in by tetramethylammonium ions. (2010) (15)
An exact lattice model of complex solutions: Chemical potentials depend on solute and solvent shape (1995) (15)
Hydrophobicity in a simple model of water: solvation and hydrogen bond energies (1998) (15)
Convex Global Underestimation for Molecular Structure Prediction (2001) (14)
Computational linguistics: A new tool for exploring biopolymer structures and statistical mechanics (2007) (14)
The effect of multiple binding modes on empirical modeling of ligand docking to proteins (1999) (14)
Statistical mechanics of helix bundles using a dynamic programming approach. (2007) (14)
Short-range interactions: from simple ions to polyelectrolyte solutions (2004) (14)
Computer simulations of ionenes, hydrophobic ions with unusual solution thermodynamic properties. The ion-specific effects. (2009) (13)
Stochastic innovation as a mechanism by which catalysts might self-assemble into chemical reaction networks (2007) (13)
Predicting Protein Dimer Structures Using MELD × MD. (2019) (13)
Statistical thermodynamic theory for the melting of n-alkanes from their rotator phases (1985) (13)
How Do Cells Adapt? Stories Told in Landscapes. (2020) (13)
RNA Folding Transitions and Cooperativity (2001) (13)
Opposing Pressures of Speed and Efficiency Guide the Evolution of Molecular Machines (2019) (13)
Rotational superposition and least squares: The SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller (2005) (12)
Response to “Comment on ‘The Mechanism of Hydrophobic Solvation Depends on Solute Radius', J. Phys. Chem. B 2000, 104, 1326” (2001) (12)
Conformational Entropy and Protein Stability (1988) (12)
Coordinate‐space formulation of polymer lattice cluster theory (1993) (12)
Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge (2014) (12)
Explicit-water molecular dynamics study of a short-chain 3,3 ionene in solutions with sodium halides. (2009) (12)
Molecular conformations in surfactant micelles (1985) (12)
MELD × MD Folds Nonthreadables, Giving Native Structures and Populations. (2018) (11)
Modeling the Overproduction of Ribosomes when Antibacterial Drugs Act on Cells (2015) (11)
Modeling simple alcohols in two dimensions (2006) (11)
A method for parameter optimization in computational biology. (2000) (11)
CryoFold: determining protein structures and data-guided ensembles from cryo-EM density maps. (2021) (10)
Concentration Dependence of the Viscosity and Viscoelasticity of Polymer Solutions: Application of the Theory of Muthukumar and Freed (1980) (10)
Modeling beta‐sheet peptide‐protein interactions: Rosetta FlexPepDock in CAPRI rounds 38‐45 (2019) (10)
Iterative assembly of helical proteins by optimal hydrophobic packing. (2008) (10)
Monte Carlo on the manifold and MD refinement for binding pose prediction of protein–ligand complexes: 2017 D3R Grand Challenge (2018) (10)
Small molecule solvation changes due to the presence of salt are governed by the cost of solvent cavity formation and dispersion. (2014) (10)
Protein surgery. (1987) (10)
Dynamics of Polymer Solutions. 3. An Instrument for Stress Relaxations on Dilute Solutions of Large Polymer Molecules (1980) (10)
MELD-Path Efficiently Computes Conformational Transitions, Including Multiple and Diverse Paths. (2018) (10)
Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations. (2015) (10)
Maximum Caliber : a general variational principle for dynamical systems (2018) (9)
Computing ligands bound to proteins using MELD-accelerated MD. (2020) (9)
Extracting representative structures from protein conformational ensembles (2014) (9)
TRIFORCE: Tessellated Semianalytical Solvent Exposed Surface Areas and Derivatives (2014) (8)
Analytical theory of the hydrophobic effect of solutes in water. (2017) (8)
Erratum: “The effects of internal constraints on the configurations of chain molecules” [J. Chem. Phys. 92, 3118 (1990)] (1997) (8)
Protein structure prediction and potential energy landscape analysis using continuous global minimization (1997) (8)
Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution (2020) (7)
Phospholipid interactions in model membrane systems (2005) (7)
Interactions in dilute monolayers of long-chain ions at the interface between n-heptane and aqueous salt solutions (1986) (7)
Statistical mechanics of chain molecules at interfaces (1991) (7)
Citation histories of papers: sometimes the rich get richer, sometimes they don't (2017) (7)
Extracting Microscopic Energies from Oil-Phase Solvation Experiments (2000) (7)
A Grammatical Theory for the Conformational Changes of Simple Helix Bundles (2006) (7)
The Refractory Period Matters: Unifying Mechanisms of Macroscopic Brain Waves (2020) (7)
Special Section On Multiscale Modeling In Biology (2006) (6)
Evolution of mechanical cooperativity among myosin II motors (2021) (6)
Theory for Radii and Second Virial Coefficients. 1. Highly Charged Polyelectrolytes (1995) (6)
Energy Landscape Projections of Molecular Potential Functions (2000) (6)
Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4 (2019) (6)
Inferring a network from dynamical signals at its nodes (2020) (6)
Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules (2016) (5)
Building Markov state models using optimal transport theory. (2018) (5)
Molecular Modeling for Drug Discovery (2017) (5)
Correction to “Charge Asymmetries in Hydration of Polar Solutes” (2011) (5)
Proteostasis is adaptive: Balancing chaperone holdases against foldases (2020) (5)
Parameter optimization for the Gaussian model of protein folding (2002) (5)
Modeling Hofmeister Effects. (2009) (5)
Erratum: Enhanced structure in polymers at interfaces [J. Chem. Phys. 94, 8542 (1991)] (1992) (5)
ClusPro in rounds 38 to 45 of CAPRI: Toward combining template‐based methods with free docking (2020) (5)
Driving forces in the origins of life (2021) (4)
Metabolism modulates network synchrony in the aging brain (2021) (4)
Water in the hydrocarbon core of micelles (reply) (1985) (4)
DILL Side-chain entropy and packing in proteins (1994) (3)
Modeling the solvation of nonpolar amino acids in guanidinium chloride solutions. (2014) (3)
Dynamics of Polymer Solutions. 4. Shear-Stress-Relaxation Experiments on Solutions of DNA from Bacteriophage T2 (1980) (3)
Dynamics of Polymer Solutions. 2. The Determination of Molecular Weight Distribution by Viscoelasticity (1980) (3)
Dynamics of Polymer Solutions. 1. Theory for an Instrument (1980) (3)
Molecular Organization in Amphiphilic Aggregates (1984) (3)
Accelerating Protein Folding Molecular Dynamics Using Inter-Residue Distances from Machine Learning Servers (2022) (3)
Minimal constraints for maximum caliber analysis of dissipative steady-state systems. (2019) (3)
Meld: Modeling Peptide-Protein Interactions (2013) (3)
Fluorescence and kinetic studies on the divalent metal ion induced conformational changes in DNase a. (1981) (3)
Treating sequence dependence of protein stability in a mean‐field model (1998) (3)
CryoFold: Ab-initio structure determination from electron density maps using molecular dynamics (2019) (2)
Preface: Special Topic on Coarse Graining of Macromolecules, Biopolymers, and Membranes. (2015) (2)
New Concepts Stabilization of Proteins in Confined Spaces † (2)
CryoFold: determining protein structures and ensembles from cryo-EM data (2019) (2)
Younger, but not older, brains are poised at a critical point of functional activity (2020) (2)
Ion pairing in molecular simulations of aqueous alkali halide solutions. (2009) (2)
The protein folding problem: Searching conformations of compact chain molecule (1995) (2)
How did prebiotic polymers become informational foldamers (2016) (2)
Metabolism modulates global synchrony in the aging brain (2020) (2)
Hydrophobic Zippers: A Conformational Search Strategy for Proteins (1994) (1)
Analytical 2-Dimensional Model of Nonpolar and Ionic Solvation in Water. (2021) (1)
Lattice models in the study of protein design (1992) (1)
Inverse Protein Folding. (1998) (1)
MAINMAST-MELD-MDFF: Denovo Structure-Determination with Data-Guided Molecular Dynamics (2019) (1)
Integrative Modeling of Protein Conformational Ensembles using Limited Data (2013) (1)
Resultants and loop closure - eScholarship (2006) (1)
Nanoscale Catalyst Chemotaxis Can Drive the Assembly of Functional Pathways (2021) (1)
Using Physics and Heuristics in Protein Structure Prediction (2015) (1)
Bacterial Growth and Division: Theory (2014) (1)
Protein folding and chart parsing (2006) (1)
BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions (2022) (1)
Darwinian evolution as a dynamical principle. (2023) (1)
Inferring transition rates on networks with incomplete knowledge (2015) (1)
Constraint methods that accelerate free-energy simulations of biomolecules. (2015) (1)
Dynamics in dissipative systems. And, their Maximum Caliber trajectories in a solvable model (2019) (1)
Iterative Assembly of Protein Fragments (2010) (1)
Theory for Protein Aggregation (1992) (1)
Partitioning of nonpolar solutes into bilayers and amorphous n-alkanes [Erratum to document cited in CA112(8):63160d] (1990) (1)
Hierarchy of anomalies in the two-dimensional Mercedes-Benz model of water. (2018) (1)
Editorial: In Memory of Peter A. Kollman (2003) (1)
Correction: Folding Very Short Peptides Using Molecular Dynamics (2006) (1)
Erratum: Intrachain loops in polymers: Effects of excluded volume [J. Chem. Phys. 90, 492 (1989)] (1992) (1)
Ketone Diets Can Reverse Some Brain Activities that are Lost in Aging (2020) (1)
Accelerating Molecular Dynamics Enrichments of High-Affinity Ligands for Proteins. (2021) (1)
MELD-accelerated molecular dynamics help determine amyloid fibril structures (2021) (1)
Molecular Simulations Find Stable Structures in Fragments of Protein G. (2008) (1)
Biodistribution of an activatable cell-penetrating SPECT imaging probe for prostate cancer in mice study (2007) (1)
Competition between counterion entropy and local binding selects dimensionality of charged nanostructures (2010) (1)
Determining Protein Structures using Accelerated MD Simulations and Noisy Data (2020) (1)
The Semi-Explicit Assembly Solvation Approach and Selected Applications (2012) (0)
Acknowledgement to Reviewers (2004) (0)
Protein folding rates and pathways based on native state topology (2002) (0)
Biological Actions Arise from Protein Motions (2017) (0)
Autobiography of Ken A. Dill. (2018) (0)
Predicting the conformational preferences of proteins using a physics-based free energy method (2014) (0)
MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands. (2023) (0)
Max Delbruck Prize in Biological Physics Talk: The Physics of Cellular Proteostasis (2019) (0)
Inferring microscopic kinetics of a Markov process using maximum caliber (2014) (0)
Growth behaviors of bacteria reveal the evolutionary significance of energy-efficiency (2015) (0)
Trade Offs between Energy Generation and Maintenance Drive Cellular Biogenesis at High Growth Rates (2014) (0)
Crustwater: Modeling Hydrophobic Solvation (2022) (0)
Protein Folding Transition States as Eigenstates (2005) (0)
Solution Dynamics of Monoclonal Antibodies: Experimental and Computational Approach (2010) (0)
Global Minimization and Parameter Estimation in Computational Biology (2001) (0)
Thieno[3,2-b]thiophene in complex with T4 lysozyme L99A/M102Q (2009) (0)
Enhancing MD simulations of proteins using vague and combinatorics information (2016) (0)
Meld Folds Nonthreadable Proteins (2018) (0)
2-ethoxy-3,4-dihydro-2h-pyran in complex with T4 lysozyme L99A/M102Q (2009) (0)
MELD-accelerated molecular dynamics help determine amyloid fibril structures (2021) (0)
171 Protein structure prediction with limited data (2013) (0)
of an independent within-subject experiment of healthy, young adults scanned at resting state while on glycolytic and ketogenic diets (27). Ketone bodies decrease the relative free energy of adenosine triphosphate (ATP) production by approximately 27% (2021) (0)
Predicting the Toggle Switch Bistability from Maximum Uncertainty Principles (2010) (0)
4,5,6,7-tetrahydroindole in complex with T4 lysozyme L99A/M102Q (2009) (0)
Power-law distribution functions derived from maximum entropy and a symmetry relationship (2011) (0)
Hydophobic Guided Protein Folding (2014) (0)
Some Cell Behavior is Encoded in Proteome Physics (2016) (0)
Physical Constraints on Proteomes Impose Limits to Biological Evolution (2014) (0)
Faculty Opinions recommendation of Experimental accuracy in protein structure refinement via molecular dynamics simulations. (2019) (0)
Author response for "ClusPro in rounds 38‐45 of CAPRI: Toward combining template‐based methods with free docking" (2019) (0)
Molecular Simulations and Conformational Sampling (2017) (0)
The Large Scale Parallelization of a Conformational 3D Protein Structure Prediction Application (1998) (0)
A Kinemati View of Loop (2009) (0)
Physics Based Protein Structure Refinement (2012) (0)
Origins of life: first came evolutionary dynamics (2023) (0)
A microscopic theory of solvation of monoions. (2012) (0)
Selected Publications of Ken A. Dill. (2018) (0)
Resultants and Loop Closure [ 1 ] (0)
Proteins Have Stable Equilibrium Conformations (2017) (0)
THE PROTEIN FOLDING PROBLEM Understanding and predicting the three-dimensional structures of proteins from their sequences of amino acids requires both basic knowledge of molecular forces and sophisticated computer programs that search for the correct configurations. (1993) (0)
Acknowledgement to Reviewers of Life in 2017 (2018) (0)
Amorphous polymers: general discussion (1979) (0)
Accurate Solutions with the Semi-Explicit Assembly Water Model (2012) (0)
A Minimal Model of the E. Coli Bacterium in Exponential Phase Growth (2013) (0)
Cooperativity: the Helix–Coil, Ising, & Landau Models (2010) (0)
The chain conformations in membranes and micelles. (1986) (0)
Thermodynamic Stability of an Aging Proteome (2014) (0)
Folding and Aggregation Are Cooperative Transitions (2017) (0)
Interface : Addressing new challenges in computational biology (2009) (0)
Inferring Protein Structures from Sparse and Ambiguous Data (2014) (0)
Colleagues of Ken A. Dill. (2018) (0)
Molecular dynamics simulation study of solvent effects on conformation and dynamics of polyethylene oxide and polypropylene oxide chains in water and in common organic solvents (2014) (0)
The Nonequilibrium Statistical Thermodynamics of Biological Cycles (2016) (0)
The Scientific Life of Vojko Vlachy (2017) (0)
Proteins Are Polymers That Fold into Specific Structures (2017) (0)
The Second Law and Biology (2008) (0)
Faculty of 1000 evaluation for Unbiased molecular dynamics of 11 min timescale drug unbinding reveals transition state stabilizing interactions. (2018) (0)
The Biology-Combinatorics Interface: Addressing new challenges in computational biology (2008) (0)
1 CONVEX GLOBAL UNDERESTIMATION FOR MOLECULAR STRUCTURE PREDICTION (1997) (0)
Combining Physics and Knowledge in Blind Protein Structure Prediction (2016) (0)
Proteins Perform Cellular Functions (2017) (0)
Computing Poses of Ligands Bound to Proteins using MELD Accelerated Molecular Dynamics (2020) (0)
Predicting Protein Structures from Sequences (2017) (0)
Evolutionary Tradeoffs in Efficiency and Turnover Rate for F 0 F 1 -ATPase (2018) (0)
2-methoxyphenol in complex with T4 lysozyme L99A/M102Q (2009) (0)
How Do Bacterial Growth Rates Relate to Evolutionary Fitness Landscapes for Energy-Efficiency? (2015) (0)
Protein Geometries and Energetics (2017) (0)
2-ethylphenol in complex with T4 lysozyme L99A/M102Q (2009) (0)
Improving Protein Structure Prediction by Smoothing Energy Functions (2010) (0)
Nitrosobenzene in complex with T4 lysozyme L99A/M102Q (2009) (0)
Supporting Information for “Growth rates of protein crystals” (2011) (0)
A Central Role for Peptides and Proteins in the Chemistry to Biology Transition of the Origins of Life (2020) (0)
Topology based theory of helix-coil transition (2006) (0)
The Principles of Protein Folding Kinetics (2017) (0)
Extracting Kinetic Models from Single Molecule Experiments by Direct Inference (2012) (0)
Molecular Motors have Evolved to Optimize Thermodynamic Performance (2017) (0)
A Mi cros co pic Theory of Sol va tion of Mo no ions (2012) (0)
Reply to Vazquez: Optimal density is robust to variations in calculation (2012) (0)
Capturing the Roles of Attraction and Shape in Nonpolar Solvation (2010) (0)
Might DNA Shape Tell Proteins How to Fold (1994) (0)
Theory of the Solubility of Protein Crystals (2010) (0)
N ov 2 00 3 Cooperativity in Two-State Protein Folding Kinetics (2007) (0)
2-methylphenol in complex with T4 lysozyme L99A/M102Q (2009) (0)
Computing solvent-induced forces in the solvation approach called Semi Explicit Assembly (2014) (0)
Designing RNA folding cooperativity (1999) (0)
Routes are trees : The parsing view on protein folding (0)
Computation of Atomic Solvent Accessible Surface Areas and Gradients for the Calculation of Solvation Energy and Forces on Molecules (2014) (0)
Nonequilibrium statistical physics beyond the ideal heat bath approximation. (2022) (0)
Faculty Opinions recommendation of Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations. (2017) (0)
(Z)-Thiophene-2-carboxaldoxime in complex with T4 lysozyme L99A/M102Q (2009) (0)
La biología y las ciencias básicas (2001) (0)
Faculty of 1000 evaluation for Complete protein-protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling. (2018) (0)
4-chloro-1h-pyrazole in complex with T4 lysozyme L99A/M102Q (2009) (0)
Faculty Opinions recommendation of Monitoring 15N Chemical Shifts During Protein Folding by Pressure-Jump NMR. (2018) (0)
STEREOCHEMISTRY OF GADOLINIUM(3+) AND MANGANESE(2+) INTERACTIONS WITH D-GLUCONAMIDE DERIVATIVES BY CARBON-13 NMR SPECTROSCOPY (1985) (0)
Adaptive Boundaries in Multi-Resolution Simulations (2015) (0)
Percolation Theory Identifies Critical Constraints on White Matter Tract Development (2022) (0)
A New Semi-Explicit Solvation Model: Fast Physics for Better Results (2010) (0)
DENl\TURED STATES OF PROTEINS (1991) (0)
The Bootstrap Model of Prebiotic Networks of Proteins and Nucleic Acids (2022) (0)
Using Delaunay Tessellation of Proteins to Improve Current ENM (2012) (0)
Heat, Work, & Energy (2010) (0)
Measurement of FLux Fluctuations in Diffusion in the Small-Numbers Limit (2006) (0)
Nonequilibrium Statistical Mechanics Using Maximum Entropy Methods (2005) (0)
Investigation of Smart Responses of Human Serum Albumin in Fever Condition: An In Vitro Approach (2014) (0)
A Simple Model of Protein Folding Kinetics Based on Native Topology (2012) (0)
2019 EMDataResource Model Metrics Challenge Dataset (2020) (0)
Faculty Opinions recommendation of Past-future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics. (2019) (0)
Extremum Principles Predict Equilibria (2010) (0)
5-chloro-2-methylphenol in complex with T4 lysozyme L99A/M102Q (2009) (0)
Rotational Superposition and least squares : SVD or Quaternions ? Reply to the preceding comment by G . Kneller (0)
Benzylacetate in complex with T4 lysozyme L99A/M102Q (2009) (0)
Caliber approach for non-equilibrium systems with a small number of states (2008) (0)
Maximum caliber is a general variational principle for nonequilibrium statistical mechanics (2021) (0)
Proteins and other Foldameric Materials (2008) (0)

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