Ken A. Dill

Publication Activity (10 Years)

Years Active: 1997-2023
Publications (10 Years): 8

Top Topics

Grand Challenges

Steady State Simulation

Binding Peptides

Academic Papers

Top Venues

J. Comput. Aided Mol. Des.

PLoS Comput. Biol.

J. Chem. Inf. Model.

Publications

Sridip Parui, James C. Robertson, Sandeep Somani, Gary Tresadern, Cong Liu, Ken A. Dill
MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands. J. Chem. Inf. Model. 63 (9) (2023)
Corey Weistuch, Luca Agozzino, Lilianne R. Mujica-Parodi, Ken A. Dill
Inferring a network from dynamical signals at its nodes. PLoS Comput. Biol. 16 (11) (2020)
Sergei Kotelnikov, Andrey Alekseenko, Cong Liu, Mikhail Ignatov, Dzmitry Padhorny, Emiliano Brini, Mark Lukin, Evangelos A. Coutsias, Ken A. Dill, Dima Kozakov
Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4. J. Comput. Aided Mol. Des. 34 (2) (2020)
Adam M. R. de Graff, David E. Mosedale, Tilly Sharp, Ken A. Dill, David J. Grainger
Proteostasis is adaptive: Balancing chaperone holdases against foldases. PLoS Comput. Biol. 16 (12) (2020)
Mikhail Ignatov, Cong Liu, Andrey Alekseenko, Zhuyezi Sun, Dzmitry Padhorny, Sergei Kotelnikov, Andrey M. Kazennov, Ivan Grebenkin, Yaroslav Kholodov, Istvan Kolosvari, Alberto Pérez, Ken A. Dill, Dima Kozakov
Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge. J. Comput. Aided Mol. Des. 33 (1) (2019)
Michael J. Hazoglu, Vivek Kulkarni, Steven Skiena, Ken A. Dill
Citation histories of papers: sometimes the rich get richer, sometimes they don't. CoRR (2017)
Emiliano Brini, S. Shanaka Paranahewage, Christopher J. Fennell, Ken A. Dill
Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules. J. Comput. Aided Mol. Des. 30 (11) (2016)
Steve Pressé, Kingshuk Ghosh, Julian Lee, Ken A. Dill
Reply to C. Tsallis' "Conceptual Inadequacy of the Shore and Johnson Axioms for Wide Classes of Complex Systems". Entropy 17 (7) (2015)
Libo Li, Ken A. Dill, Christopher J. Fennell
Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge. J. Comput. Aided Mol. Des. 28 (3) (2014)
Charles W. Kehoe, Christopher J. Fennell, Ken A. Dill
Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test. J. Comput. Aided Mol. Des. 26 (5) (2012)
G. J. Peterson, Ken A. Dill
Power-law distribution functions derived from maximum entropy and a symmetry relationship CoRR (2011)
G. J. Peterson, Steve Pressé, Ken A. Dill
Nonuniversal power law scaling in the probability distribution of scientific citations CoRR (2010)
Vincent A. Voelz, M. Scott Shell, Ken A. Dill
Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments. PLoS Comput. Biol. 5 (2) (2009)
John D. Chodera, William C. Swope, Jed W. Pitera, Ken A. Dill
Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations. Multiscale Model. Simul. 5 (4) (2006)
Julia Hockenmaier, Aravind K. Joshi, Ken A. Dill
Protein folding and chart parsing. EMNLP (2006)
Bosco K. Ho, Ken A. Dill
Folding Very Short Peptides Using Molecular Dynamics. PLoS Comput. Biol. 2 (4) (2006)
David Chiang, Aravind K. Joshi, Ken A. Dill
A Grammatical Theory for the Conformational Changes of Simple Helix Bundles. J. Comput. Biol. 13 (1) (2006)
Bosco K. Ho, Ken A. Dill
Correction: Folding Very Short Peptides Using Molecular Dynamics. PLoS Comput. Biol. 2 (5) (2006)
Tamar Schlick, Ken A. Dill
Special Section On Multiscale Modeling In Biology. Multiscale Model. Simul. 5 (4) (2006)
Evangelos A. Coutsias, Chaok Seok, Ken A. Dill
Rotational superposition and least squares: The SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller. J. Comput. Chem. 26 (15) (2005)
Evangelos A. Coutsias, Chaok Seok, Ken A. Dill
Using quaternions to calculate RMSD. J. Comput. Chem. 25 (15) (2004)
Evangelos A. Coutsias, Chaok Seok, Matthew P. Jacobson, Ken A. Dill
A kinematic view of loop closure. J. Comput. Chem. 25 (4) (2004)
Guang Song, Shawna L. Thomas, Ken A. Dill, J. Martin Scholtz, Nancy M. Amato
A Path Planning-Based Study of Protein Folding with a Case Study of Hairpin Formation in Protein G and L. Pacific Symposium on Biocomputing (2003)
Nancy M. Amato, Ken A. Dill, Guang Song
Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures. J. Comput. Biol. 10 (3/4) (2003)
Chaok Seok, J. Ben Rosen, John D. Chodera, Ken A. Dill
MOPED: Method for optimizing physical energy parameters using decoys. J. Comput. Chem. 24 (1) (2003)
Nancy M. Amato, Ken A. Dill, Guang Song
Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures. RECOMB (2002)
Keith D. Ball, Burak Erman, Ken A. Dill
The elastic net algorithm and protein structure prediction. J. Comput. Chem. 23 (1) (2002)
K. W. Foreman, Andrew T. Phillips, J. Ben Rosen, Ken A. Dill
Comparing search strategies for finding global optima on energy landscapes. J. Comput. Chem. 20 (14) (1999)
Philip F. LoCascio, Kaizhi Yue, Peter Cummings, Ken A. Dill
The Large Scale Parallelization of a Conformational 3D Protein Structure Prediction Application. SC (1998)
Ken A. Dill, Andrew T. Phillips, J. Ben Rosen
Protein Structure and Energy Landscape Dependence on Sequence Using a Continuous Energy Function. J. Comput. Biol. 4 (3) (1997)
Ken A. Dill, Andrew T. Phillips, J. Ben Rosen
Protein structure prediction and potential energy landscape analysis using continuous global minimization. RECOMB (1997)