Kenneth Dill, PhD
Professor Emeritus
Pharmaceutical Chemistry
School of Pharmacy

Websites

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• Dill Lab at Laufer Center (dillgroup.org)

Grants and Projects

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• Solvation modeling for next-gen biomolecule simulations, NIH, 2020-2025
• MELD: accelerating MD modeling of proteins using Bayesian inference, NIH, 2018-2021
• Modeling Aqueous Solvation in Biology, NIH, 2001-2019
• Combinatorial Statistical Mechanics of Protein Folding, NIH, 1985-2012
• Modeling Aqueous Solvation in Biology, NIH, 2001-2010
• Protein Stability Theory, NIH, 1991-1995
• Head Group Interactions in Membranes and Micelles, NIH, 1988-1992
• Statistical Mechanics of Amphiphilic Aggregates, NIH, 1983-1986

Publications (193)

Top publication keywords:
EntropyChemistry, PhysicalHydrophobic and Hydrophilic InteractionsWaterModels, ChemicalProteinsModels, MolecularBiophysicsThermodynamicsMolecular Dynamics SimulationSolventsModels, TheoreticalComputer SimulationProtein ConformationProtein Folding

• Computational Procedure for Predicting Excipient Effects on Protein-Protein Affinities.
  Journal of chemical theory and computation 2024 Dignon GL, Dill KA
• A computational procedure for predicting excipient effects on protein-protein affinities.
  bioRxiv : the preprint server for biology 2023 Dignon GL, Dill KA
• MHC-Fine: Fine-tuned AlphaFold for Precise MHC-Peptide Complex Prediction.
  bioRxiv : the preprint server for biology 2023 Glukhov E, Kalitin D, Stepanenko D, Zhu Y, Nguyen T, Jones G, Simmerling C, Mitchell JC, Vajda S, Dill KA, Padhorny D, Kozakov D
• Protein Association in Solution: Statistical Mechanical Modeling.
  Biomolecules 2023 Vlachy V, Kalyuzhnyi YV, Hribar-Lee B, Dill KA
• Transcriptional drift in aging cells: A global de-controller.
  bioRxiv : the preprint server for biology 2023 Matsuzaki T, Weistuch C, de Graff A, Dill KA, Balázsi G

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• Brain signaling becomes less integrated and more segregated with age.
  bioRxiv : the preprint server for biology 2023 Razban RM, Antal BB, Dill KA, Mujica-Parodi LR
• Computing Free Energies of Fold-Switching Proteins Using MELD x MD.
  Journal of chemical theory and computation 2023 Parui S, Brini E, Dill KA
• Simple Model of Liquid Water Dynamics.
  The journal of physical chemistry. B 2023 Urbic T, Dill KA
• Next-Gen Biophysics: Look to the Forest, Beyond the Trees.
  Annual review of biophysics 2023 Schmit J, Dill KA
• MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands.
  Journal of chemical information and modeling 2023 Parui S, Robertson JC, Somani S, Tresadern G, Liu C, Dill KA
• Cancer heterogeneity is defined by normal cellular trade-offs.
  bioRxiv : the preprint server for biology 2023 Weistuch C, Murgas KA, Zhu J, Norton L, Dill KA, Deasy JO, Tannenbaum AR
• Early path dominance as a principle for neurodevelopment.
  Proceedings of the National Academy of Sciences of the United States of America 2023 Razban RM, Pachter JA, Dill KA, Mujica-Parodi LR
• Origins of life: first came evolutionary dynamics.
  QRB discovery 2023 Kocher C, Dill KA
• Darwinian evolution as a dynamical principle.
  Proceedings of the National Academy of Sciences of the United States of America 2023 Kocher CD, Dill KA
• Nonequilibrium statistical physics beyond the ideal heat bath approximation.
  Physical review. E 2023 Pachter JA, Dill KA
• BioMThermDB 1.0: Thermophysical Database of Proteins in Solutions.
  International journal of molecular sciences 2022 Nikolic M, Brudar S, Coutsias E, Dill KA, Lukšic M, Simmerling C, Hribar-Lee B
• Review of the application of Kirchhoff's Laws of series and parallel flows to pharmacology: Defining organ clearance.
  Pharmacology & therapeutics 2022 Pachter JA, Dill KA, Sodhi JK, Benet LZ
• Crustwater: Modeling Hydrophobic Solvation.
  The journal of physical chemistry. B 2022 Yadav AK, Bandyopadhyay P, Coutsias EA, Dill KA
• The Bootstrap Model of Prebiotic Networks of Proteins and Nucleic Acids.
  Life (Basel, Switzerland) 2022 Farquharson T, Agozzino L, Dill K
• Accelerating Protein Folding Molecular Dynamics Using Inter-Residue Distances from Machine Learning Servers.
  Journal of chemical theory and computation 2022 Nassar R, Brini E, Parui S, Liu C, Dignon GL, Dill KA
• Accelerating Molecular Dynamics Enrichments of High-Affinity Ligands for Proteins.
  Journal of chemical theory and computation 2021 Liu C, Brini E, Dill KA
• Metabolism modulates network synchrony in the aging brain.
  Proceedings of the National Academy of Sciences of the United States of America 2021 Weistuch C, Mujica-Parodi LR, Razban RM, Antal B, van Nieuwenhuizen H, Amgalan A, Dill KA
• CryoFold: determining protein structures and data-guided ensembles from cryo-EM density maps.
  Matter 2021 Shekhar M, Terashi G, Gupta C, Sarkar D, Debussche G, Sisco NJ, Nguyen J, Mondal A, Vant J, Fromme P, Van Horn WD, Tajkhorshid E, Kihara D, Dill K, Perez A, Singharoy A
• MELD-accelerated molecular dynamics help determine amyloid fibril structures.
  Communications biology 2021 Sharma B, Dill KA
• Nanoscale Catalyst Chemotaxis Can Drive the Assembly of Functional Pathways.
  The journal of physical chemistry. B 2021 Kocher C, Agozzino L, Dill K
• The Protein Folding Problem: The Role of Theory.
  Journal of molecular biology 2021 Nassar R, Dignon GL, Razban RM, Dill KA
• Evolution of mechanical cooperativity among myosin II motors.
  Proceedings of the National Academy of Sciences of the United States of America 2021 Wagoner JA, Dill KA
• The Refractory Period Matters: Unifying Mechanisms of Macroscopic Brain Waves.
  Neural computation 2021 Weistuch C, Mujica-Parodi LR, Dill K
• Analytical 2-Dimensional Model of Nonpolar and Ionic Solvation in Water.
  The journal of physical chemistry. B 2021 Yadav AK, Bandyopadhyay P, Urbic T, Dill KA
• Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge.
  Nature methods 2021 Lawson CL, Kryshtafovych A, Adams PD, Afonine PV, Baker ML, Barad BA, Bond P, Burnley T, Cao R, Cheng J, Chojnowski G, Cowtan K, Dill KA, DiMaio F, Farrell DP, Fraser JS, Herzik MA, Hoh SW, Hou J, …
• Proteostasis is adaptive: Balancing chaperone holdases against foldases.
  PLoS computational biology 2020 de Graff AM, Mosedale DE, Sharp T, Dill KA, Grainger DJ
• Inferring a network from dynamical signals at its nodes.
  PLoS computational biology 2020 Weistuch C, Agozzino L, Mujica-Parodi LR, Dill KA
• Protein storytelling through physics.
  Science (New York, N.Y.) 2020 Brini E, Simmerling C, Dill K
• Computing Ligands Bound to Proteins Using MELD-Accelerated MD.
  Journal of chemical theory and computation 2020 Liu C, Brini E, Perez A, Dill KA
• How Do Cells Adapt? Stories Told in Landscapes.
  Annual review of chemical and biomolecular engineering 2020 Agozzino L, Balázsi G, Wang J, Dill KA
• ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking.
  Proteins 2020 Padhorny D, Porter KA, Ignatov M, Alekseenko A, Beglov D, Kotelnikov S, Ashizawa R, Desta I, Alam N, Sun Z, Brini E, Dill K, Schueler-Furman O, Vajda S, Kozakov D
• Diet modulates brain network stability, a biomarker for brain aging, in young adults.
  Proceedings of the National Academy of Sciences of the United States of America 2020 Mujica-Parodi LR, Amgalan A, Sultan SF, Antal B, Sun X, Skiena S, Lithen A, Adra N, Ratai EM, Weistuch C, Govindarajan ST, Strey HH, Dill KA, Stufflebeam SM, Veech RL, Clarke K
• The Maximum Caliber Variational Principle for Nonequilibria.
  Annual review of physical chemistry 2020 Ghosh K, Dixit PD, Agozzino L, Dill KA
• Modeling beta-sheet peptide-protein interactions: Rosetta FlexPepDock in CAPRI rounds 38-45.
  Proteins 2020 Khramushin A, Marcu O, Alam N, Shimony O, Padhorny D, Brini E, Dill KA, Vajda S, Kozakov D, Schueler-Furman O
• Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4.
  Journal of computer-aided molecular design 2019 Kotelnikov S, Alekseenko A, Liu C, Ignatov M, Padhorny D, Brini E, Lukin M, Coutsias E, Dill KA, Kozakov D
• Opposing Pressures of Speed and Efficiency Guide the Evolution of Molecular Machines.
  Molecular biology and evolution 2019 Wagoner JA, Dill KA
• Proteostasis collapse is a driver of cell aging and death.
  Proceedings of the National Academy of Sciences of the United States of America 2019 Santra M, Dill KA, de Graff AMR
• NMR-assisted protein structure prediction with MELDxMD.
  Proteins 2019 Robertson JC, Nassar R, Liu C, Brini E, Dill KA, Perez A
• Minimal constraints for maximum caliber analysis of dissipative steady-state systems.
  Physical review. E 2019 Agozzino L, Dill K
• Predicting Protein Dimer Structures Using MELD × MD.
  Journal of chemical theory and computation 2019 Brini E, Kozakov D, Dill KA
• Mechanisms for achieving high speed and efficiency in biomolecular machines.
  Proceedings of the National Academy of Sciences of the United States of America 2019 Wagoner JA, Dill KA
• Building Markov state models using optimal transport theory.
  The Journal of chemical physics 2019 Dixit PD, Dill KA
• Water Is a Cagey Liquid.
  Journal of the American Chemical Society 2018 Urbic T, Dill KA
• MELD × MD Folds Nonthreadables, Giving Native Structures and Populations.
  Journal of chemical theory and computation 2018 Robertson JC, Perez A, Dill KA
• Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge.
  Journal of computer-aided molecular design 2018 Ignatov M, Liu C, Alekseenko A, Sun Z, Padhorny D, Kotelnikov S, Kazennov A, Grebenkin I, Kholodov Y, Kolosvari I, Perez A, Dill K, Kozakov D
• Hierarchy of anomalies in the two-dimensional Mercedes-Benz model of water.
  Physical review. E 2018 Urbic T, Dill KA
• Protein evolution speed depends on its stability and abundance and on chaperone concentrations.
  Proceedings of the National Academy of Sciences of the United States of America 2018 Agozzino L, Dill KA
• How Do Chaperones Protect a Cell's Proteins from Oxidative Damage?
  Cell systems 2018 Santra M, Dill KA, de Graff AMR
• Autobiography of Ken A. Dill.
  The journal of physical chemistry. B 2018 Dill KA
• Colleagues of Ken A. Dill.
  The journal of physical chemistry. B 2018 Dill KA
• Selected Publications of Ken A. Dill.
  The journal of physical chemistry. B 2018 Dill KA
• MELD-Path Efficiently Computes Conformational Transitions, Including Multiple and Diverse Paths.
  Journal of chemical theory and computation 2018 Perez A, Sittel F, Stock G, Dill K
• Caliber Corrected Markov Modeling (C2M2): Correcting Equilibrium Markov Models.
  Journal of chemical theory and computation 2018 Dixit PD, Dill KA
• Perspective: Maximum caliber is a general variational principle for dynamical systems.
  The Journal of chemical physics 2018 Dixit PD, Wagoner J, Weistuch C, Pressé S, Ghosh K, Dill KA
• Controlling the viscosities of antibody solutions through control of their binding sites.
  Journal of molecular liquids 2017 Kastelic M, Dill KA, Kalyuzhnyi YV, Vlachy V
• How Water's Properties Are Encoded in Its Molecular Structure and Energies.
  Chemical reviews 2017 Brini E, Fennell CJ, Fernandez-Serra M, Hribar-Lee B, Lukšic M, Dill KA
• Analytical theory of the hydrophobic effect of solutes in water.
  Physical review. E 2017 Urbic T, Dill KA
• Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers.
  Proceedings of the National Academy of Sciences of the United States of America 2017 Guseva E, Zuckermann RN, Dill KA
• Why Do Fast-Growing Bacteria Enter Overflow Metabolism? Testing the Membrane Real Estate Hypothesis.
  Cell systems 2017 Szenk M, Dill KA, de Graff AMR
• Accelerating physical simulations of proteins by leveraging external knowledge.
  Wiley interdisciplinary reviews. Computational molecular science 2017 Perez A, Morrone JA, Dill KA
• Bacterial proteostasis balances energy and chaperone utilization efficiently.
  Proceedings of the National Academy of Sciences of the United States of America 2017 Santra M, Farrell DW, Dill KA
• Computed Binding of Peptides to Proteins with MELD-Accelerated Molecular Dynamics.
  Journal of chemical theory and computation 2017 Morrone JA, Perez A, MacCallum J, Dill KA
• Molecular Simulations Identify Binding Poses and Approximate Affinities of Stapled α-Helical Peptides to MDM2 and MDMX.
  Journal of chemical theory and computation 2017 Morrone JA, Perez A, Deng Q, Ha SN, Holloway MK, Sawyer TK, Sherborne BS, Brown FK, Dill KA
• Blind protein structure prediction using accelerated free-energy simulations.
  Science advances 2016 Perez A, Morrone JA, Brini E, MacCallum JL, Dill KA
• Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules.
  Journal of computer-aided molecular design 2016 Brini E, Paranahewage SS, Fennell CJ, Dill KA
• Role of Proteome Physical Chemistry in Cell Behavior.
  The journal of physical chemistry. B 2016 Ghosh K, de Graff AM, Sawle L, Dill KA
• Molecular Motors: Power Strokes Outperform Brownian Ratchets.
  The journal of physical chemistry. B 2016 Wagoner JA, Dill KA
• Modeling the Overproduction of Ribosomes when Antibacterial Drugs Act on Cells.
  Biophysical journal 2016 Maitra A, Dill KA
• Advances in free-energy-based simulations of protein folding and ligand binding.
  Current opinion in structural biology 2016 Perez A, Morrone JA, Simmerling C, Dill KA
• Constraint methods that accelerate free-energy simulations of biomolecules.
  The Journal of chemical physics 2015 Perez A, MacCallum JL, Coutsias EA, Dill KA
• Preface: Special Topic on Coarse Graining of Macromolecules, Biopolymers, and Membranes.
  The Journal of chemical physics 2015 Holm C, Gompper G, Dill KA
• Highly Charged Proteins: The Achilles' Heel of Aging Proteomes.
  Structure (London, England : 1993) 2015 de Graff AM, Hazoglou MJ, Dill KA
• Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes.
  Journal of chemical theory and computation 2015 Dixit PD, Jain A, Stock G, Dill KA
• Grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations.
  Journal of chemical theory and computation 2015 Perez A, MacCallum JL, Brini E, Simmerling C, Dill KA
• Accelerating molecular simulations of proteins using Bayesian inference on weak information.
  Proceedings of the National Academy of Sciences of the United States of America 2015 Perez A, MacCallum JL, Dill KA
• Communication: Maximum caliber is a general variational principle for nonequilibrium statistical mechanics.
  The Journal of chemical physics 2015 Hazoglou MJ, Walther V, Dixit PD, Dill KA
• Determining protein structures by combining semireliable data with atomistic physical models by Bayesian inference.
  Proceedings of the National Academy of Sciences of the United States of America 2015 MacCallum JL, Perez A, Dill KA
• Protein aggregation in salt solutions.
  Proceedings of the National Academy of Sciences of the United States of America 2015 Kastelic M, Kalyuzhnyi YV, Hribar-Lee B, Dill KA, Vlachy V
• Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations.
  Journal of chemical theory and computation 2015 Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA
• Bacterial growth laws reflect the evolutionary importance of energy efficiency.
  Proceedings of the National Academy of Sciences of the United States of America 2014 Maitra A, Dill KA
• In silico selection of therapeutic antibodies for development: viscosity, clearance, and chemical stability.
  Proceedings of the National Academy of Sciences of the United States of America 2014 Sharma VK, Patapoff TW, Kabakoff B, Pai S, Hilario E, Zhang B, Li C, Borisov O, Kelley RF, Chorny I, Zhou JZ, Dill KA, Swartz TE
• Small molecule solvation changes due to the presence of salt are governed by the cost of solvent cavity formation and dispersion.
  The Journal of chemical physics 2014 Li L, Fennell CJ, Dill KA
• Modeling the solvation of nonpolar amino acids in guanidinium chloride solutions.
  The journal of physical chemistry. B 2014 Cohen P, Dill KA, Jaswal SS
• General mechanism of two-state protein folding kinetics.
  Journal of the American Chemical Society 2014 Rollins GC, Dill KA
• TRIFORCE: Tessellated Semianalytical Solvent Exposed Surface Areas and Derivatives.
  Journal of chemical theory and computation 2014 Drechsel NJ, Fennell CJ, Dill KA, Villà-Freixa J
• Extracting representative structures from protein conformational ensembles.
  Proteins 2014 Perez A, Roy A, Kasavajhala K, Wagaman A, Dill KA, MacCallum JL
• Single molecule conformational memory extraction: p5ab RNA hairpin.
  The journal of physical chemistry. B 2014 Pressé S, Peterson J, Lee J, Elms P, MacCallum JL, Marqusee S, Bustamante C, Dill K
• Inferring Microscopic Kinetic Rates from Stationary State Distributions.
  Journal of chemical theory and computation 2014 Dixit PD, Dill KA
• Using interpolation for fast and accurate calculation of ion-ion interactions.
  The journal of physical chemistry. B 2014 Lukšic M, Fennell CJ, Dill KA
• Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge.
  Journal of computer-aided molecular design 2014 Li L, Dill KA, Fennell CJ
• Field-SEA: a model for computing the solvation free energies of nonpolar, polar, and charged solutes in water.
  The journal of physical chemistry. B 2013 Li L, Fennell CJ, Dill KA
• Computing the relative stabilities and the per-residue components in protein conformational changes.
  Structure (London, England : 1993) 2013 Roy A, Perez A, Dill KA, Maccallum JL
• A maximum entropy framework for nonexponential distributions.
  Proceedings of the National Academy of Sciences of the United States of America 2013 Peterson J, Dixit PD, Dill KA
• Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects.
  The Journal of chemical physics 2013 Rocklin GJ, Mobley DL, Dill KA, Hünenberger PH
• Nonadditive entropies yield probability distributions with biases not warranted by the data.
  Physical review letters 2013 Pressé S, Ghosh K, Lee J, Dill KA
• Blind prediction of charged ligand binding affinities in a model binding site.
  Journal of molecular biology 2013 Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA
• Calculating the sensitivity and robustness of binding free energy calculations to force field parameters.
  Journal of chemical theory and computation 2013 Rocklin GJ, Mobley DL, Dill KA
• Separated topologies--a method for relative binding free energy calculations using orientational restraints.
  The Journal of chemical physics 2013 Rocklin GJ, Mobley DL, Dill KA
• Probing antibody internal dynamics with fluorescence anisotropy and molecular dynamics simulations.
  mAbs 2013 Kortkhonjia E, Brandman R, Zhou JZ, Voelz VA, Chorny I, Kabakoff B, Patapoff TW, Dill KA, Swartz TE
• Extracting conformational memory from single-molecule kinetic data.
  The journal of physical chemistry. B 2013 Pressé S, Lee J, Dill KA
• Biophysics. Introduction.
  Annual review of biophysics 2013 Dill KA
• The protein-folding problem, 50 years on.
  Science (New York, N.Y.) 2012 Dill KA, MacCallum JL
• FlexE: Using elastic network models to compare models of protein structure.
  Journal of chemical theory and computation 2012 Perez A, Yang Z, Bahar I, Dill KA, MacCallum JL
• A microscopic theory of solvation of monoions.
  Acta chimica Slovenica 2012 Urbic T, Fennell CJ, Dill KA
• De novo structure prediction and experimental characterization of folded peptoid oligomers.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Butterfoss GL, Yoo B, Jaworski JN, Chorny I, Dill KA, Zuckermann RN, Bonneau R, Kirshenbaum K, Voelz VA
• Simulated evolution of protein-protein interaction networks with realistic topology.
  PloS one 2012 Peterson GJ, Pressé S, Peterson KS, Dill KA
• Simple model of hydrophobic hydration.
  The journal of physical chemistry. B 2012 Lukšic M, Urbic T, Hribar-Lee B, Dill KA
• Simple liquid models with corrected dielectric constants.
  The journal of physical chemistry. B 2012 Fennell CJ, Li L, Dill KA
• Growth rates of protein crystals.
  Journal of the American Chemical Society 2012 Schmit JD, Dill K
• Markov processes follow from the principle of maximum caliber.
  The Journal of chemical physics 2012 Ge H, Pressé S, Ghosh K, Dill KA
• Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test.
  Journal of computer-aided molecular design 2011 Kehoe CW, Fennell CJ, Dill KA
• Physical limits of cells and proteomes.
  Proceedings of the National Academy of Sciences of the United States of America 2011 Dill KA, Ghosh K, Schmit JD
• Physical Modeling of Aqueous Solvation.
  Journal of statistical physics 2011 Fennell CJ, Dill KA
• Assessment of protein structure refinement in CASP9.
  Proteins 2011 MacCallum JL, Pérez A, Schnieders MJ, Hua L, Jacobson MP, Dill KA
• Electrostatics and aggregation: how charge can turn a crystal into a gel.
  The Journal of chemical physics 2011 Schmit JD, Whitelam S, Dill K
• Modeling aqueous solvation with semi-explicit assembly.
  Proceedings of the National Academy of Sciences of the United States of America 2011 Fennell CJ, Kehoe CW, Dill KA
• What drives amyloid molecules to assemble into oligomers and fibrils?
  Biophysical journal 2011 Schmit JD, Ghosh K, Dill K
• Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER.
  Biopolymers 2011 Voelz VA, Dill KA, Chorny I
• Cellular proteomes have broad distributions of protein stability.
  Biophysical journal 2010 Ghosh K, Dill K
• Receptacle model of salting-in by tetramethylammonium ions.
  The journal of physical chemistry. B 2010 Hribar-Lee B, Dill KA, Vlachy V
• Nonuniversal power law scaling in the probability distribution of scientific citations.
  Proceedings of the National Academy of Sciences of the United States of America 2010 Peterson GJ, Pressé S, Dill KA
• A statistical mechanical theory for a two-dimensional model of water.
  The Journal of chemical physics 2010 Urbic T, Dill KA
• Aqueous alkali halide solutions: can osmotic coefficients be explained on the basis of the ionic sizes alone?
  Physical chemistry chemical physics : PCCP 2010 Kalyuzhnyi YV, Vlachy V, Dill KA
• The stabilities of protein crystals.
  The journal of physical chemistry. B 2010 Schmit JD, Dill KA
• Oil/water transfer is partly driven by molecular shape, not just size.
  Journal of the American Chemical Society 2010 Fennell CJ, Kehoe C, Dill KA
• Theory for the three-dimensional Mercedes-Benz model of water.
  The Journal of chemical physics 2009 Bizjak A, Urbic T, Vlachy V, Dill KA
• Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site.
  Journal of molecular biology 2009 Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill KA, Shoichet BK
• Trajectory approach to two-state kinetics of single particles on sculpted energy landscapes.
  Physical review letters 2009 Wu D, Ghosh K, Inamdar M, Lee HJ, Fraser S, Dill K, Phillips R
• Computing protein stabilities from their chain lengths.
  Proceedings of the National Academy of Sciences of the United States of America 2009 Ghosh K, Dill KA
• Ion pairing in molecular simulations of aqueous alkali halide solutions.
  The journal of physical chemistry. B 2009 Fennell CJ, Bizjak A, Vlachy V, Dill KA
• Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".
  Structure (London, England : 1993) 2009 Mobley DL, Dill KA
• Predictions of hydration free energies from all-atom molecular dynamics simulations.
  The journal of physical chemistry. B 2009 Mobley DL, Bayly CI, Cooper MD, Dill KA
• Modeling Hofmeister Effects.
  Acta chimica Slovenica 2009 Hribar-Lee B, Vlachy V, Dill KA
• Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations.
  Journal of chemical theory and computation 2009 Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA
• Predicting peptide structures in native proteins from physical simulations of fragments.
  PLoS computational biology 2009 Voelz VA, Shell MS, Dill KA
• Blind test of physics-based prediction of protein structures.
  Biophysical journal 2009 Shell MS, Ozkan SB, Voelz V, Wu GA, Dill KA
• Assessment of the protein-structure refinement category in CASP8.
  Proteins 2009 MacCallum JL, Hua L, Schnieders MJ, Pande VS, Jacobson MP, Dill KA
• Development of an optimized activatable MMP-14 targeted SPECT imaging probe.
  Bioorganic & medicinal chemistry 2008 Watkins GA, Jones EF, Scott Shell M, VanBrocklin HF, Pan MH, Hanrahan SM, Feng JJ, He J, Sounni NE, Dill KA, Contag CH, Coussens LM, Franc BL
• Iterative assembly of helical proteins by optimal hydrophobic packing.
  Structure (London, England : 1993) 2008 Wu GA, Coutsias EA, Dill KA
• Biomimetic nanostructures: creating a high-affinity zinc-binding site in a folded nonbiological polymer.
  Journal of the American Chemical Society 2008 Lee BC, Chu TK, Dill KA, Zuckermann RN
• Maximum Caliber: a variational approach applied to two-state dynamics.
  The Journal of chemical physics 2008 Stock G, Ghosh K, Dill KA
• A test on peptide stability of AMBER force fields with implicit solvation.
  The journal of physical chemistry. B 2008 Shell MS, Ritterson R, Dill KA
• Charge asymmetries in hydration of polar solutes.
  The journal of physical chemistry. B 2008 Mobley DL, Baker JR, Barber AE, Fennell CJ, Dill KA
• Molecular Simulations Find Stable Structures in Fragments of Protein G.
  Acta chimica Slovenica 2008 Urbic T, Urbic T, Avbelj F, Dill KA
• Treating entropy and conformational changes in implicit solvent simulations of small molecules.
  The journal of physical chemistry. B 2008 Mobley DL, Dill KA, Chodera JD
• The protein folding problem.
  Annual review of biophysics 2008 Dill KA, Ozkan SB, Shell MS, Weikl TR
• The ultimate speed limit to protein folding is conformational searching.
  Journal of the American Chemical Society 2007 Ghosh K, Ozkan SB, Dill KA
• Protein folding by zipping and assembly.
  Proceedings of the National Academy of Sciences of the United States of America 2007 Ozkan SB, Wu GA, Chodera JD, Dill KA
• The protein folding problem: when will it be solved?
  Current opinion in structural biology 2007 Dill KA, Ozkan SB, Weikl TR, Chodera JD, Voelz VA
• Predicting absolute ligand binding free energies to a simple model site.
  Journal of molecular biology 2007 Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA
• Stochastic innovation as a mechanism by which catalysts might self-assemble into chemical reaction networks.
  Proceedings of the National Academy of Sciences of the United States of America 2007 Bradford JA, Dill KA
• Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.
  The Journal of chemical physics 2007 Chodera JD, Singhal N, Pande VS, Dill KA, Swope WC
• Statistical mechanics of helix bundles using a dynamic programming approach.
  Journal of the American Chemical Society 2007 Lucas A, Huang L, Joshi A, Dill KA
• Exploring zipping and assembly as a protein folding principle.
  Proteins 2007 Voelz VA, Dill KA
• Measuring flux distributions for diffusion in the small-numbers limit.
  The journal of physical chemistry. B 2007 Seitaridou E, Inamdar MM, Phillips R, Ghosh K, Dill K
• Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.
  The journal of physical chemistry. B 2007 Mobley DL, Dumont E, Chodera JD, Dill KA
• Routes are trees: the parsing perspective on protein folding.
  Proteins 2007 Hockenmaier J, Joshi AK, Dill KA
• The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change.
  Journal of chemical theory and computation 2007 Mobley DL, Chodera JD, Dill KA
• Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations.
  Journal of chemical theory and computation 2007 Chodera JD, Swope WC, Pitera JW, Seok C, Dill KA
• Transition-states in protein folding kinetics: the structural interpretation of Phi values.
  Journal of molecular biology 2006 Weikl TR, Dill KA
• On the use of orientational restraints and symmetry corrections in alchemical free energy calculations.
  The Journal of chemical physics 2006 Mobley DL, Chodera JD, Dill KA
• Folding very short peptides using molecular dynamics.
  PLoS computational biology 2006 Ho BK, Dill KA
• Teaching the principles of statistical dynamics.
  American journal of physics 2006 Ghosh K, Dill KA, Inamdar MM, Seitaridou E, Phillips R
• A grammatical theory for the conformational changes of simple helix bundles.
  Journal of computational biology : a journal of computational molecular cell biology 2006 Chiang D, Joshi AK, Dill KA
• Surfaces affect ion pairing.
  The journal of physical chemistry. B 2005 Chorny I, Dill KA, Jacobson MP
• Water's hydrogen bonds in the hydrophobic effect: a simple model.
  The journal of physical chemistry. B 2005 Xu H, Dill KA
• Rotational superposition and least squares: the SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller.
  Journal of computational chemistry 2005 Coutsias EA, Seok C, Dill KA
• Folding a nonbiological polymer into a compact multihelical structure.
  Journal of the American Chemical Society 2005 Lee BC, Zuckermann RN, Dill KA
• 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 Merlo C, Dill KA, Weikl TR
• The flexibility in the proline ring couples to the protein backbone.
  Protein science : a publication of the Protein Society 2005 Ho BK, Coutsias EA, Seok C, Dill KA
• Comprehensive analysis of protein folding activation thermodynamics reveals a universal behavior violated by kinetically stable proteases.
  Journal of molecular biology 2005 Jaswal SS, Truhlar SM, Dill KA, Agard DA
• Modeling water, the hydrophobic effect, and ion solvation.
  Annual review of biophysics and biomolecular structure 2005 Dill KA, Truskett TM, Vlachy V, Hribar-Lee B
• Using quaternions to calculate RMSD.
  Journal of computational chemistry 2004 Coutsias EA, Seok C, Dill KA
• A kinematic view of loop closure.
  Journal of computational chemistry 2004 Coutsias EA, Seok C, Jacobson MP, Dill KA
• Cooperativity in two-state protein folding kinetics.
  Protein science : a publication of the Protein Society 2004 Weikl TR, Palassini M, Dill KA
• Incorporation of chemoselective functionalities into peptoids via solid-phase submonomer synthesis.
  Bioconjugate chemistry 2004 Horn T, Lee BC, Dill KA, Zuckermann RN
• Structural and spectroscopic studies of peptoid oligomers with alpha-chiral aliphatic side chains.
  Journal of the American Chemical Society 2003 Wu CW, Kirshenbaum K, Sanborn TJ, Patch JA, Huang K, Dill KA, Zuckermann RN, Barron AE
• Fast protein folding kinetics.
  Proceedings of the National Academy of Sciences of the United States of America 2003 Schonbrun J, Dill KA
• Folding kinetics of two-state proteins: effect of circularization, permutation, and crosslinks.
  Journal of molecular biology 2003 Weikl TR, Dill KA
• A simple analytical model of water.
  Biophysical chemistry 2003 Truskett TM, Dill KA
• Folding rates and low-entropy-loss routes of two-state proteins.
  Journal of molecular biology 2003 Weikl TR, Dill KA
• MOPED: method for optimizing physical energy parameters using decoys.
  Journal of computational chemistry 2003 Seok C, Rosen JB, Chodera JD, Dill KA
• 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 Song G, Thomas S, Dill KA, Scholtz JM, Amato NM
• Computing the transition state populations in simple protein models.
  Biopolymers 2003 Ozkan SB, Dill KA, Bahar I
• 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 Amato NM, Dill KA, Song G
• Potential of mean force between two hydrophobic solutes in water.
  Biophysical chemistry 2002 Southall NT, Dill KA
• Fast-folding protein kinetics, hidden intermediates, and the sequential stabilization model.
  Protein science : a publication of the Protein Society 2002 Ozkan SB, Dill KA, Bahar I
• The elastic net algorithm and protein structure prediction.
  Journal of computational chemistry 2002 Ball KD, Erman B, Dill KA