List of works by Ken A. Dill

A Simple Model of Water and the Hydrophobic Effect

scientific article (publication date: April 1998)

A View of the Hydrophobic Effect

A View of the Hydrophobic Effect

A fast conformational search strategy for finding low energy structures of model proteins

scientific article published on October 1996

A grammatical theory for the conformational changes of simple helix bundles

scientific article

A kinematic view of loop closure

scientific article

A lattice statistical mechanics model of the conformational and sequence spaces of proteins

article

A maximum entropy framework for nonexponential distributions ⬇️

scientific article (publication date: 17 December 2013)

A method for parameter optimization in computational biology

scientific article

A microscopic theory of solvation of monoions.

scientific article

A path planning-based study of protein folding with a case study of hairpin formation in protein G and L.

scientific article published in January 2003

A rhelogical separator for very large DNA molecules ⬇️

scientific article published on October 10, 1979

A simple analytical model of water.

scientific article published on September 2003

A simple model of chaperonin-mediated protein folding

scientific article

A simple protein folding algorithm using a binary code and secondary structure constraints.

scientific article published in August 1995

A statistical mechanical model for hydrogen exchange in globular proteins

scientific article

A statistical mechanical theory for a two-dimensional model of water

scientific article published on June 2010

A test of lattice protein folding algorithms

scientific article

A test on peptide stability of AMBER force fields with implicit solvation

scientific article

A two-dimensional model of water: Solvation of nonpolar solutes

article

A two-dimensional model of water: Theory and computer simulations

article

Accelerating Molecular Dynamics Enrichments of High-Affinity Ligands for Proteins

scientific article published on 08 December 2021

Accelerating Protein Folding Molecular Dynamics Using Inter-Residue Distances from Machine Learning Servers

scientific article published on 08 February 2022

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

scientific article

Accelerating physical simulations of proteins by leveraging external knowledge.

scientific article

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

scientific article published on 8 September 2016

Additivity principles in biochemistry

scientific article published on January 1997

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

scientific article

Aggregation and denaturation of apomyoglobin in aqueous urea solutions

scientific article published in April 1993

An improved thermodynamic perturbation theory for Mercedes-Benz water.

scientific article

An iterative method for extracting energy-like quantities from protein structures.

scientific article published on October 1996

Analytical theory of the hydrophobic effect of solutes in water

scientific article

Aqueous alkali halide solutions: can osmotic coefficients be explained on the basis of the ionic sizes alone?

scientific article published on 20 April 2010

Are proteins well-packed?

scientific article

Assessment of protein structure refinement in CASP9.

scientific article

Assessment of the protein-structure refinement category in CASP8

scientific article

Autobiography of Ken A. Dill

scientific article published on 01 May 2018

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics

scientific article published in April 2007

Bacterial growth laws reflect the evolutionary importance of energy efficiency

scientific article

Bacterial proteostasis balances energy and chaperone utilization efficiently

scientific article

Binding of ionic ligands to polyelectrolytes

scientific article published on October 1996

Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".

scientific article published on April 2009

Biomimetic nanostructures: creating a high-affinity zinc-binding site in a folded nonbiological polymer

scientific article published on July 2008

Biophysics. Introduction

scientific article published in January 2013

Blind Prediction of Charged Ligand Binding Affinities in a Model Binding Site

scientific article

Blind protein structure prediction using accelerated free-energy simulations

scientific article

Blind test of physics-based prediction of protein structures.

scientific article

Building Markov State Models Using Optimal Transport Theory

Building Markov state models using optimal transport theory

scientific article published on 01 February 2019

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

scientific article

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

scientific article published on July 2013

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

scientific article published on 11 January 2018

Cellular proteomes have broad distributions of protein stability

scientific article

Chain molecules at high densities at interfaces

scientific article published on January 1988

Charge asymmetries in hydration of polar solutes.

scientific article published on 6 February 2008

Charge effects on folded and unfolded proteins

scientific article

Chiral N-substituted glycines can form stable helical conformations

scientific article published on 01 January 1997

ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking

scientific article published on 06 March 2020

Colleagues of Ken A. Dill

scientific article published on 01 May 2018

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

scientific article published in August 2015

Comparing folding codes for proteins and polymers

scientific article published in March 1996

Comparison of Charge Models for Fixed-Charge Force Fields: Small Molecule Hydration Free Energies in Explicit Solvent

Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

scientific article published on 10 February 2007

Comprehensive analysis of protein folding activation thermodynamics reveals a universal behavior violated by kinetically stable proteases

scientific article published on 28 January 2005

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

scientific article published on 2 January 2017

Computer Simulations of Ionenes, Hydrophobic Ions with Unusual Solution Thermodynamic Properties. The Ion-Specific Effects

article published in 2009

Computing ligands bound to proteins using MELD-accelerated MD

scientific article published on 10 September 2020

Computing protein stabilities from their chain lengths

scientific article published on 17 June 2009

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

scientific article

Computing the transition state populations in simple protein models

scientific article

Confined water: a Mercedes-Benz model study

scientific article published on 01 March 2006

Constraint methods that accelerate free-energy simulations of biomolecules

scientific article

Constraint-based assembly of tertiary protein structures from secondary structure elements

scientific article published on October 2000

Controlling the viscosities of antibody solutions through control of their binding sites

scientific article published on 21 November 2017

Cooperativity in protein-folding kinetics ⬇️

scientific article published on March 1, 1993

Cooperativity in two-state protein folding kinetics.

scientific article

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

scientific article published in March 2015

Correction: Folding Very Short Peptides Using Molecular Dynamics.

scientific article published on 26 May 2006

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

scientific article published on 04 February 2021

De novo structure prediction and experimental characterization of folded peptoid oligomers.

scientific article

Decisions in force field development: an alternative to those described by Roterman et al. (J. Biomol. Struct. Dyn. 7, 421 (1989)).

scientific article published in June 1991

Denatured states of proteins

scientific article published on January 1991

Designing amino acid sequences to fold with good hydrophobic cores

scientific article published in December 1995

Designing polymers that mimic biomolecules

scientific article

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

scientific article

Development of an optimized activatable MMP-14 targeted SPECT imaging probe.

scientific article published on 06 December 2008

Diet modulates brain network stability, a biomarker for brain aging, in young adults

scientific article published on 03 March 2020

Does compactness induce secondary structure in proteins? A study of poly-alanine chains computed by distance geometry

scientific article published in August 1994

Dominant forces in protein folding

scientific article (publication date: 7 August 1990)

Dynamical fluctuations in biochemical reactions and cycles

scientific article published on 15 September 2010

Electrostatics and aggregation: how charge can turn a crystal into a gel.

scientific article

Explicit-water molecular dynamics study of a short-chain 3,3 ionene in solutions with sodium halides

scientific article published on April 2009

Exploring zipping and assembly as a protein folding principle

scientific article published in March 2007

Extracting conformational memory from single-molecule kinetic data

scientific article

Extracting representative structures from protein conformational ensembles.

scientific article published on 5 July 2014

Families and the structural relatedness among globular proteins

scientific article published on June 1993

Fast protein folding kinetics

scientific article published on 20 October 2003

Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model

scientific article

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

scientific article published on 13 December 2013

FlexE: Using elastic network models to compare models of protein structure.

scientific article

Fluorescence and kinetic studies on the divalent metal ion induced conformational changes in DNase a ⬇️

scientific article published on June 10, 1981

Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers

scientific article published on 22 August 2017

Folding a nonbiological polymer into a compact multihelical structure

scientific article published in August 2005

Folding and binding

scientific article published in February 1996

Folding kinetics of two-state proteins: effect of circularization, permutation, and crosslinks.

scientific article published in September 2003

Folding proteins with a simple energy function and extensive conformational searching

scientific article published on February 1996

Folding rates and low-entropy-loss routes of two-state proteins.

scientific article published in June 2003

Folding very short peptides using molecular dynamics

scientific article

Forces of tertiary structural organization in globular proteins

scientific article

Frequency dependence of NMR spin lattice relaxation in bilayer membranes

From Levinthal to pathways to funnels

scientific article

General mechanism of two-state protein folding kinetics

scientific article

Great organizing principles

scientific article published in October 1996

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

scientific article published on 17 September 2015

Growth rates of protein crystals

scientific article published on 23 February 2012

Hierarchy of anomalies in the two-dimensional Mercedes-Benz model of water

scientific article published on 11 September 2018

Highly Charged Proteins: The Achilles' Heel of Aging Proteomes

scientific article published on 24 December 2015

How Do Cells Adapt? Stories Told in Landscapes

scientific article published on 01 June 2020

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

scientific article published on 06 June 2018

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

scientific article published on 26 September 2017

How ions affect the structure of water

scientific article published on October 2002

Hydrogen bonding in globular proteins

scientific article published on August 20, 1992

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

scientific article

Incorporation of chemoselective functionalities into peptoids via solid-phase submonomer synthesis

scientific article published in March 2004

Inferring Microscopic Kinetic Rates from Stationary State Distributions

scientific article

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

scientific article published on 02 October 2015

Inferring a network from dynamical signals at its nodes

scientific article published on 30 November 2020

Interphases of chain molecules: Monolayers and lipid bilayer membranes

scientific article

Inverse protein folding problem: designing polymer sequences

scientific article published on May 1992

Ion pairing in molecular simulations of aqueous alkali halide solutions

scientific article published on May 2009

Ion pairing in molecular simulations of aqueous alkali halide solutions

scientific article published on November 2009

Iterative assembly of helical proteins by optimal hydrophobic packing.

scientific article

Lateral interactions among phosphatidylcholine and phosphatidylethanolamine head groups in phospholipid monolayers and bilayers ⬇️

scientific article published on May 3, 1988

Ligand binding to proteins: the binding landscape model

scientific article

Local and nonlocal interactions in globular proteins and mechanisms of alcohol denaturation

scientific article published on December 1993

Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics Simulations

article

MELD x MD Folds Nonthreadables, Giving Native Structures and Populations

scientific article published on 21 November 2018

MELD-Path Efficiently Computes Conformational Transitions, Including Multiple and Diverse Paths.

scientific article

MOPED: method for optimizing physical energy parameters using decoys.

scientific article published in January 2003

Markov processes follow from the principle of maximum caliber

scientific article published on February 2012

Maximum Caliber: a variational approach applied to two-state dynamics

scientific article published in May 2008

Measuring flux distributions for diffusion in the small-numbers limit

scientific article published on 13 February 2007

Mechanisms for achieving high speed and efficiency in biomolecular machines

scientific article published on 08 March 2019

Minimal constraints for maximum caliber analysis of dissipative steady-state systems

scientific article published on 01 July 2019

Modeling Hofmeister Effects.

scientific article published on March 2009

Modeling aqueous solvation with semi-explicit assembly

scientific article

Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45

scientific article published on 31 December 2019

Modeling compact denatured states of proteins

scientific article published on 01 May 1994

Modeling protein stability as heteropolymer collapse.

scientific article published on January 1995

Modeling stochastic dynamics in biochemical systems with feedback using maximum caliber

scientific article published on 27 April 2011

Modeling the Overproduction of Ribosomes when Antibacterial Drugs Act on Cells

scientific article

Modeling the effects of mutations on the denatured states of proteins ⬇️

scientific article published on February 1, 1992

Modeling the solvation of nonpolar amino acids in guanidinium chloride solutions

scientific article published on 28 August 2014

Modeling water, the hydrophobic effect, and ion solvation

scientific article

Models of cooperativity in protein folding

scientific article

Molecular Motors: Power Strokes Outperform Brownian Ratchets.

scientific article published on 17 May 2016

Molecular Simulations Find Stable Structures in Fragments of Protein G.

scientific article

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

scientific article published on 2 January 2017

Molecular organization in micelles and vesicles

scientific article

Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge

scientific article published on 12 November 2018

NMR determination of the major solution conformation of a peptoid pentamer with chiral side chains

scientific article

NMR-assisted protein structure prediction with MELDxMD

scientific article published on 08 August 2019

Native protein fluctuations: the conformational-motion temperature and the inverse correlation of protein flexibility with protein stability

scientific article published in October 1998

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

scientific article

Nonuniversal power law scaling in the probability distribution of scientific citations

scientific article

Oil/water transfer is partly driven by molecular shape, not just size

scientific article published on January 2010

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

scientific article

Opposing Pressures of Speed and Efficiency Guide the Evolution of Molecular Machines

scientific article published on 01 December 2019

Origins of structure in globular proteins

scientific article

Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER.

scientific article published in January 2011

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

scientific article published in January 2018

Phi values in protein-folding kinetics have energetic and structural components.

scientific article

Phospholipid interactions in model membrane systems. I. Experiments on monolayers

scientific article

Phospholipid interactions in model membrane systems. II. Theory

scientific article

Physical Modeling of Aqueous Solvation

scientific article

Physical limits of cells and proteomes

scientific article published on 17 October 2011

Polymer principles and protein folding

scientific article

Polymer principles in protein structure and stability.

scientific article

Potential of mean force between two hydrophobic solutes in water

scientific article

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

scientific article

Predicting Protein Dimer Structures Using MELD × MD

scientific article published on 05 April 2019

Predicting absolute ligand binding free energies to a simple model site

scientific article

Predicting conformational switches in proteins

scientific article

Predicting peptide structures in native proteins from physical simulations of fragments

scientific article

Predicting the structures of 18 peptides using Geocore

scientific article published on April 1999

Predictions of hydration free energies from all-atom molecular dynamics simulations.

scientific article published in April 2009

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

scientific article published in December 2015

Principles of protein folding--a perspective from simple exact models.

scientific article

Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations

scientific article published on 8 February 2013

Protein Structure and Energy Landscape Dependence on Sequence Using a Continuous Energy Function ⬇️

scientific article published on January 1, 1997

Protein aggregation in salt solutions

scientific article published on 11 May 2015

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

article published in the Proceedings of the National Academy of Sciences of the United States of America

Protein folding by zipping and assembly

scientific article

Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics

scientific article published on January 1998

Protein stability: electrostatics and compact denatured states

scientific article published on May 1991

Protein storytelling through physics

scientific article published on 01 November 2020

Protein surgery.

scientific article published in October 1987

Proteostasis collapse is a driver of cell aging and death

scientific article published on 16 October 2019

Proteostasis is adaptive: Balancing chaperone holdases against foldases

scientific article published on 14 December 2020

RNA folding energy landscapes.

scientific article

Receptacle Model of Salting-In by Tetramethylammonium Ions ⬇️

scientific article published on October 28, 2010

Reply to C. Tsallis’ “Conceptual Inadequacy of the Shore and Johnson Axioms for Wide Classes of Complex Systems”

scientific article published on 17 July 2015

Reply to Vazquez: Optimal density is robust to variations in calculation.

scientific article published on 17 February 2012

Response to “Comment on ‘The Mechanism of Hydrophobic Solvation Depends on Solute Radius',J.Phys. Chem. B2000,104, 1326”

article

Retention mechanisms of reversed-phase liquid chromatography: determination of solute-solvent interaction free energies

scientific article published on 01 November 1989

Role of Proteome Physical Chemistry in Cell Behavior

scientific article

Rotational superposition and least squares: the SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller

scientific article

Routes are trees: the parsing perspective on protein folding.

scientific article

Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4

scientific article published on 26 December 2019

Selected Publications of Ken A. Dill

scientific article published on 01 May 2018

Separated topologies--a method for relative binding free energy calculations using orientational restraints

scientific article published on February 2013

Sequence-specific polypeptoids: a diverse family of heteropolymers with stable secondary structure

scientific article

Sequence-structure relationships in proteins and copolymers

scientific article published on 01 September 1993

Side-chain entropy and packing in proteins

scientific article

Simple liquid models with corrected dielectric constants

scientific article published on 21 March 2012

Simple model of hydrophobic hydration

scientific article published on 21 May 2012

Simulated evolution of protein-protein interaction networks with realistic topology ⬇️

scientific article

Single molecule conformational memory extraction: p5ab RNA hairpin

scientific article published on 5 June 2014

Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations

scientific article

Small molecule solvation changes due to the presence of salt are governed by the cost of solvent cavity formation and dispersion.

scientific article published on December 2014

Solute partitioning into lipid bilayer membranes

scientific article

Solvation: how to obtain microscopic energies from partitioning and solvation experiments ⬇️

scientific article published on January 1, 1997

Solvent denaturation and stabilization of globular proteins

scientific article published in June 1991

Stabilization of Proteins in Confined Spaces†

scientific article published on 01 September 2001

Statistical mechanics of helix bundles using a dynamic programming approach.

scientific article

Statistical potentials extracted from protein structures: how accurate are they?

scientific article published in March 1996

Stochastic innovation as a mechanism by which catalysts might self-assemble into chemical reaction networks

scientific article (publication date: 12 June 2007)

Strengthening biomedicine's roots

scientific article published on July 1999

Structural and Spectroscopic Studies of Peptoid Oligomers with α-Chiral Aliphatic Side Chains ⬇️

scientific article published on November 5, 2003

Surfaces affect ion pairing

scientific article published in December 2005

TRIFORCE: Tessellated Semianalytical Solvent Exposed Surface Areas and Derivatives

scientific article published on 23 July 2014

Teaching the principles of statistical dynamics

scientific article

Temperature dependence of retention in reversed-phase liquid chromatography. 2. Mobile-phase considerations

scientific article published on 01 July 1992

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

scientific article published on 29 January 2014

Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test.

scientific article

The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change

scientific article

The Maximum Caliber Variational Principle for Nonequilibria

scientific article published on 19 February 2020

The Mechanism of Hydrophobic Solvation Depends on Solute Radius

The chain conformations in membranes and micelles

scientific article

The effect of multiple binding modes on empirical modeling of ligand docking to proteins

scientific article published on May 1999

The elastic net algorithm and protein structure prediction.

scientific article

The flexibility in the proline ring couples to the protein backbone

scientific article

The meaning of hydrophobicity

scientific article

The protein folding problem

scientific article

The protein folding problem: when will it be solved?

scientific article

The protein-folding problem, 50 years on.

scientific article

The stabilities of protein crystals

scientific article published on March 2010

The three states of globular proteins: acid denaturation

scientific article published in November 1991

The ultimate speed limit to protein folding is conformational searching

scientific article published on 7 September 2007

Theory for protein folding cooperativity: helix bundles

scientific article published on February 2009

Theory for protein mutability and biogenesis

scientific article (publication date: 1990)

Theory for the folding and stability of globular proteins

scientific article

Theory for the separation of very large DNA molecules by radial migration

scientific article published in November 1979

Theory for the solvation of nonpolar solutes in water.

scientific article published in November 2007

Theory for the three-dimensional Mercedes-Benz model of water

scientific article published on November 2009

Thermal stabilities of globular proteins

scientific article

Trajectory approach to two-state kinetics of single particles on sculpted energy landscapes.

scientific article published on 31 July 2009

Transition states and the meaning of Phi-values in protein folding kinetics

scientific article

Transition-states in protein folding kinetics: the structural interpretation of Phi values

scientific article published on 28 October 2006

Treating entropy and conformational changes in implicit solvent simulations of small molecules

scientific article published on 3 January 2008

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

scientific article published in January 2007

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

scientific article

Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures

scientific article published on 01 January 2003

Using quaternions to calculate RMSD

scientific article

Water Is a Cagey Liquid ⬇️

scientific article published on 03 December 2018

Water's hydrogen bonds in the hydrophobic effect: a simple model

scientific article

What drives amyloid molecules to assemble into oligomers and fibrils?

scientific article

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

scientific article

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