Ken A. Dill

发表

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

Charles W. Kehoe, Christopher J. Fennell, Ken A. Dill, 2012, Journal of Computer-Aided Molecular Design.

MOPED: Method for optimizing physical energy parameters using decoys

J. Ben Rosen, Chaok Seok, John D. Chodera, 2003, J. Comput. Chem..

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

Christopher J. Fennell, Ken A. Dill, Libo Li, 2014, Journal of Computer-Aided Molecular Design.

Annual review of biophysics

James R. Williamson, Xiaowei Zhuang, Ken A. Dill, 2008 .

TRIFORCE: Tessellated Semianalytical Solvent Exposed Surface Areas and Derivatives

Jordi Villà-Freixa, Christopher J. Fennell, Ken A. Dill, 2014, Journal of chemical theory and computation.

A Grammatical Theory for the Conformational Changes of Simple Helix Bundles

Aravind K. Joshi, David Chiang, Ken A. Dill, 2006, J. Comput. Biol..

The elastic net algorithm and protein structure prediction

Burak Erman, Ken A. Dill, Keith D. Ball, 2002, J. Comput. Chem..

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

Andrey Alekseenko, Dima Kozakov, Ken A. Dill, 2019, Journal of Computer-Aided Molecular Design.

Comparing search strategies for finding global optima on energy landscapes

J. Ben Rosen, Andrew T. Phillips, Ken A. Dill, 1999, J. Comput. Chem..

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

Christopher J. Fennell, Ken A. Dill, Emiliano Brini, 2016, Journal of Computer-Aided Molecular Design.

Extracting Kinetic Models from Single Molecule Experiments by Direct Inference

Justin L. MacCallum, Steve Pressé, Julian Lee, 2012 .

CryoFold: Ab-initio structure determination from electron density maps using molecular dynamics

Genki Terashi, Daisuke Kihara, Petra Fromme, 2019 .

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

Cong Liu, Dima Kozakov, Yaroslav Kholodov, 2018, Journal of Computer-Aided Molecular Design.

Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution

Genki Terashi, Daisuke Kihara, Grigore D. Pintilie, 2020, bioRxiv.

Citation histories of papers: sometimes the rich get richer, sometimes they don't pdf

Steven Skiena, Vivek Kulkarni, Ken A. Dill, 2017, ArXiv.

Reply to C. Tsallis' "Conceptual Inadequacy of the Shore and Johnson Axioms for Wide Classes of Complex Systems"

Kingshuk Ghosh, Steve Pressé, Julian Lee, 2015, Entropy.

The Large Scale Parallelization of a Conformational 3D Protein Structure Prediction Application

Philip F. LoCascio, Ken A. Dill, Kaizhi Yue, 1998, Proceedings of the IEEE/ACM SC98 Conference.

Author response for "ClusPro in rounds 38‐45 of CAPRI: Toward combining template‐based methods with free docking"

Dima Kozakov, Dmitri Beglov, Sandor Vajda, 2019 .

Inverse Protein Folding.

Ken A. Dill, 1998 .

Power-law distribution functions derived from maximum entropy and a symmetry relationship pdf

Ken A. Dill, G. J. Peterson, K. Dill, 2011, ArXiv.

Hydophobic Guided Protein Folding

Justin L. MacCallum, Ken A. Dill, Alberto Perez, 2014 .

Glossary of Terms used in Photochemistry

Allen J. Bard, Erik W. Thulstrup, Bernard Valeur, 2003 .

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

J. Ben Rosen, Andrew T. Phillips, Ken A. Dill, 1997, J. Comput. Biol..

Determining Protein Structures using Accelerated MD Simulations and Noisy Data

Ken A. Dill, Alberto Perez, Emiliano Brini, 2020 .

Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures

Nancy M. Amato, Guang Song, Ken A. Dill, 2003, J. Comput. Biol..

Correction: Folding Very Short Peptides Using Molecular Dynamics

Ken A. Dill, Bosco K. Ho, 2006, PLoS Comput. Biol..

Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments

Ken A. Dill, M. Scott Shell, Vincent A. Voelz, 2009, PLoS Comput. Biol..

Nonuniversal power law scaling in the probability distribution of scientific citations

Steve Pressé, Ken A. Dill, G. J. Peterson, 2010, Proceedings of the National Academy of Sciences.

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

Nancy M. Amato, Guang Song, Ken A. Dill, 2002, RECOMB '02.

Protein structure prediction and potential energy landscape analysis using continuous global minimization

J. Ben Rosen, Andrew T. Phillips, Ken A. Dill, 1997, RECOMB '97.

A Path Planning-Based Study of Protein Folding with a Case Study of Hairpin Formation in Protein G and L

Nancy M. Amato, Guang Song, Shawna L. Thomas, 2002, Pacific Symposium on Biocomputing.

Physics Based Protein Structure Refinement

Justin L. MacCallum, Ken A. Dill, Alberto Perez, 2012 .

Adaptive Boundaries in Multi-Resolution Simulations

Vijay S. Pande, Ken A. Dill, Jason A. Wagoner, 2015 .

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.

Hue Sun Chan, Ken A. Dill, 1993 .

Using Delaunay Tessellation of Proteins to Improve Current ENM

Justin L. MacCallum, Evangelos A. Coutsias, Ken A. Dill, 2012 .

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

Chaok Seok, Evangelos A. Coutsias, Ken A. Dill, 2005, J. Comput. Chem..

A kinematic view of loop closure

Chaok Seok, Evangelos A. Coutsias, Ken A. Dill, 2004, J. Comput. Chem..

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

John D. Chodera, Ken A. Dill, Jed W. Pitera, 2006, Multiscale Model. Simul..

Inferring Microscopic Kinetic Rates from Stationary State Distributions

Ken A. Dill, Purushottam D. Dixit, K. Dill, 2014, Journal of chemical theory and computation.

Special Section On Multiscale Modeling In Biology

Tamar Schlick, Ken A. Dill, K. Dill, 2006, Multiscale Model. Simul..

Protein folding and chart parsing

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

Folding Very Short Peptides Using Molecular Dynamics

Ken A. Dill, Bosco K. Ho, K. Dill, 2006, PLoS Comput. Biol..

Enhancing MD simulations of proteins using vague and combinatorics information

Ken A. Dill, 2016 .

Enhanced structure in polymers at interfaces

Hue Sun Chan, Ken A. Dill, Victor A. Bloomfield, 1991 .

Molecular Structure Prediction by Global Optimization

Ken A. Dill, K. Dill, A. Phillips, 1997 .

Symmetries in proteins: A knot theory approach

Ken A. Dill, Shi-Jie Chen, K. Dill, 1996 .

Resultants and loop closure - eScholarship

Chaok Seok, Michael J. Wester, Evangelos A. Coutsias, 2006 .

Maximum Caliber : a general variational principle for dynamical systems

Kingshuk Ghosh, Ken A. Dill, Steve Pressé, 2018 .

Simulated Evolution of Protein-Protein Interaction Networks with Realistic Topology

Ken A. Dill, Steve Pressé, G. J. Peterson, 2012, PloS one.

Molecular conformations in surfactant micelles

Ken A. Dill, Sow-Hsin Chen, James D. Dill, 1984, Nature.

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

Ivet Bahar, Ken A. Dill, S. Banu Ozkan, 2001, Nature Structural Biology.

A Simple Model of Water and the Hydrophobic Effect

Ken A. Dill, Kevin A. T. Silverstein, A. D. J. Haymet, 1998 .

Field-SEA: A Model for Computing the Solvation Free Energies of Nonpolar, Polar, and Charged Solutes in Water

Christopher J. Fennell, Ken A. Dill, K. Dill, 2013, The journal of physical chemistry. B.

Gaussian model of protein folding

Burak Erman, Ken A. Dill, K. Dill, 2000 .

Symmetry and designability for lattice protein models

Ken A. Dill, Ned S. Wingreen, Tairan Wang, 2000 .

Theory for the conformational changes of double-stranded chain molecules

Ken A. Dill, Shi-Jie Chen, K. Dill, 1998 .

Theory for the aggregation of proteins and copolymers

Ken A. Dill, Gregg B. Fields, K. Dill, 1992 .

Computational linguistics: A new tool for exploring biopolymer structures and statistical mechanics

Aravind K. Joshi, David Chiang, Julia Hockenmaier, 2007 .

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

Ken A. Dill, Thomas W. Patapoff, Eric Hilario, 2014, Proceedings of the National Academy of Sciences.

Iterative Assembly of Protein Fragments

Justin L. MacCallum, Ken A. Dill, Geoffrey C. Rollins, 2010 .

Response to “Comment on ‘The Mechanism of Hydrophobic Solvation Depends on Solute Radius', J. Phys. Chem. B 2000, 104, 1326”

Noel Southall, Ken A. Dill, 2001 .

The molecular mechanism of retention in reversed-phase liquid chromatography

Ken A. Dill, John G. Dorsey, K. Dill, 1989 .

ChemInform Abstract: A View of the Hydrophobic Effect

Noel Southall, Ken A. Dill, A. D. J. Haymet, 2002 .

Conformations and Forces in Protein Folding

Ken A. Dill, Barry T. Nall, 1991 .

Correction to “Charge Asymmetries in Hydration of Polar Solutes”

David L. Mobley, Christopher J. Fennell, Ken A. Dill, 2011 .

The Mechanism of Hydrophobic Solvation Depends on Solute Radius

Ken A. Dill, K. Dill, Noel Southall, 2000 .

Strengthening biomedicine's roots

Ken A. Dill, K. Dill, 1999, Nature.

Aggregation of globular proteins

Ken A. Dill, K. Dill, A. Fink, 1993 .

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

David L. Mobley, Ken A. Dill, K. Dill, 2013, The Journal of chemical physics.

Energy landscapes and the collapse dynamics of homopolymers

Hue Sun Chan, Ken A. Dill, K. Dill, 1993 .

Molecular driving forces : statistical thermodynamics in biology, chemistry, physics, and nanoscience

Ken A. Dill, Sarina Bromberg, K. Dill, 2012 .

Solute partitioning into chain molecule interphases: Monolayers, bilayer membranes, and micelles

Ken A. Dill, K. Dill, J. A. Marqusee, 1986 .

RNA Folding Transitions and Cooperativity

Eivind Tøstesen, Ken A. Dill, Shi-Jie Chen, 2001 .

Solvation: Effects of molecular size and shape

Hue Sun Chan, Ken A. Dill, K. Dill, 1994 .