Ken A Dill

发表

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

Zheng Yang, Ivet Bahar, Alberto Perez, 2012, Journal of chemical theory and computation.

Blind protein structure prediction using accelerated free-energy simulations

Alberto Perez, Ken A Dill, Justin L MacCallum, 2016, Science Advances.

Routes are trees: The parsing perspective on protein folding

Julia Hockenmaier, Ken A Dill, Aravind K Joshi, 2006, Proteins.

The protein folding problem: when will it be solved?

S Banu Ozkan, Vincent A Voelz, Ken A Dill, 2007, Current opinion in structural biology.

Mechanisms for achieving high speed and efficiency in biomolecular machines

Ken A Dill, Jason A Wagoner, Jason A. Wagoner, 2019, Proceedings of the National Academy of Sciences.

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

Ken A Dill, John D Chodera, William C Swope, 2007, Journal of chemical theory and computation.

The Maximum Caliber Variational Principle for Nonequilibria.

Kingshuk Ghosh, Ken A Dill, Purushottam D Dixit, 2020, Annual review of physical chemistry.

Extracting representative structures from protein conformational ensembles

Arijit Roy, Alberto Perez, Ken A Dill, 2014, Proteins.

Extracting conformational memory from single-molecule kinetic data.

Steve Pressé, Ken A Dill, Julian Lee, 2013, The journal of physical chemistry. B.

Assessment of protein structure refinement in CASP9

Matthew P Jacobson, Ken A Dill, Justin L MacCallum, 2011, Proteins.

Building Markov state models using optimal transport theory.

Ken A Dill, Purushottam D Dixit, 2019, The Journal of chemical physics.

Computing ligands bound to proteins using MELD-accelerated MD.

Cong Liu, Alberto Perez, Ken A Dill, 2020, Journal of chemical theory and computation.

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

David L Mobley, Michael R Shirts, Ken A Dill, 2015, Journal of chemical theory and computation.

Exploring zipping and assembly as a protein folding principle

Vincent A Voelz, Ken A Dill, Vincent A. Voelz, 2006, Proteins.

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

Alberto Perez, Ken A Dill, Justin L MacCallum, 2015, Proceedings of the National Academy of Sciences.

How ions affect the structure of water.

Ken A Dill, K. Dill, Noel Southall, 2002, Journal of the American Chemical Society.

Fast protein folding kinetics

Ken A Dill, Jack Schonbrun, K. Dill, 2003, Proceedings of the National Academy of Sciences of the United States of America.

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.

David L Mobley, Ken A Dill, Philippe H Hünenberger, 2013, The Journal of chemical physics.

Computing the transition state populations in simple protein models.

S Banu Ozkan, Ivet Bahar, Ken A Dill, 2003, Biopolymers.

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

Mariola Szenk, Ken A Dill, K. Dill, 2017, Cell systems.

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

David L Mobley, Ken A Dill, John D Chodera, 2007, The journal of physical chemistry. B.

Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site.

David L Mobley, Ken A Dill, Alan P Graves, 2009, Journal of molecular biology.

Modeling water, the hydrophobic effect, and ion solvation.

Ken A Dill, Thomas M Truskett, K. Dill, 2005, Annual review of biophysics and biomolecular structure.

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

Arijit Roy, Ken A Dill, Alberto Perez, 2014, Structure.

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

Kingshuk Ghosh, Gerhard Stock, Ken A Dill, 2008, The Journal of chemical physics.

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

Ken A Dill, Joseph A Morrone, Joseph A. Morrone, 2017, Journal of chemical theory and computation.

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

Ken A Dill, Thomas R Weikl, K. Dill, 2003, Journal of molecular biology.

Computing protein stabilities from their chain lengths

Kingshuk Ghosh, Ken A Dill, K. Dill, 2009, Proceedings of the National Academy of Sciences.

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

Carlos Simmerling, Ken A Dill, Justin L MacCallum, 2015, Journal of chemical theory and computation.

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

Ken A Dill, Purushottam D Dixit, K. Dill, 2015, The Journal of chemical physics.

Charge asymmetries in hydration of polar solutes.

David L Mobley, Ken A Dill, J. R. Baker, 2008, The journal of physical chemistry. B.

Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers

Ken A Dill, K. Dill, R. Zuckermann, 2017, Proceedings of the National Academy of Sciences.

Teaching the principles of statistical dynamics.

Kingshuk Ghosh, Ken A Dill, Effrosyni Seitaridou, 2006, American journal of physics.

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

David L Mobley, Ken A Dill, John D Chodera, 2007, Journal of chemical theory and computation.

Ion pairing in molecular simulations of aqueous alkali halide solutions.

Ken A Dill, K. Dill, V. Vlachy, 2009, The journal of physical chemistry. B.

Folding a nonbiological polymer into a compact multihelical structure.

Byoung-Chul Lee, Ken A Dill, K. Dill, 2005, Journal of the American Chemical Society.

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

Kingshuk Ghosh, Steve Pressé, Ken A Dill, 2013, Physical review letters.

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

Ken A Dill, Ryan Ritterson, M Scott Shell, 2008, The journal of physical chemistry. B.

Cooperativity in two‐state protein folding kinetics

Ken A Dill, Thomas R Weikl, Matteo Palassini, 2003, Protein science : a publication of the Protein Society.

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

Charles W. Kehoe, Ken A Dill, K. Dill, 2010, Journal of the American Chemical Society.

Modeling aqueous solvation with semi-explicit assembly

Charles W. Kehoe, Ken A Dill, K. Dill, 2011, Proceedings of the National Academy of Sciences.

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

David L Mobley, Ken A Dill, Christopher I Bayly, 2009, The journal of physical chemistry. B.

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

David L Mobley, Michael R Shirts, Michael R. Shirts, 2009, Journal of chemical theory and computation.

Simple liquid models with corrected dielectric constants.

Ken A Dill, K. Dill, Libo Li, 2012, The journal of physical chemistry. B.

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

Ken A Dill, Joseph A Morrone, M Katharine Holloway, 2017, Journal of chemical theory and computation.

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

David L Mobley, Ken A Dill, K. Dill, 2013, Journal of chemical theory and computation.

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

David L Mobley, Ken A Dill, John D Chodera, 2008, The journal of physical chemistry. B.

Surfaces affect ion pairing.

Matthew P Jacobson, Ken A Dill, Ilya Chorny, 2005, The journal of physical chemistry. B.

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

Kingshuk Ghosh, Steve Pressé, Ken A Dill, 2017, The Journal of chemical physics.

Physical Modeling of Aqueous Solvation

Ken A Dill, K. Dill, C. Fennell, 2011, Journal of statistical physics.

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

Ken A Dill, Purushottam D Dixit, K. Dill, 2017, Journal of chemical theory and computation.

A simple analytical model of water.

Ken A Dill, Thomas M Truskett, K. Dill, 2003, Biophysical chemistry.

MELD × MD Folds Nonthreadables, Giving Native Structures and Populations.

Ken A Dill, Alberto Perez, James C Robertson, 2018, Journal of chemical theory and computation.

General mechanism of two-state protein folding kinetics.

Ken A Dill, Geoffrey C Rollins, K. Dill, 2014, Journal of the American Chemical Society.

Molecular Motors: Power Strokes Outperform Brownian Ratchets.

Ken A Dill, Jason A Wagoner, Jason A. Wagoner, 2016, The journal of physical chemistry. B.