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ORCIDKen A. Dill
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- affiliation: Stony Brook University, Laufer Center for Physical and Quantitative Biology and Departments of Physics and Chemistry, NY, USA
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Journal Articles
- 2023
[j23]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): 2857-2865 (2023)- 2020
- [j22]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): 179-189 (2020) - [j21]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) - [j20]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) - 2019
- [j19]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): 119-127 (2019) - 2016
- [j18]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): 1067-1077 (2016) - 2015
- [j17]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): 5043-5046 (2015) - 2014
- [j16]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): 259-264 (2014) - 2012
- [j15]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): 563-568 (2012) - 2009
- [j14]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) - 2006
- [j13]David Chiang, Aravind K. Joshi, Ken A. Dill:
A Grammatical Theory for the Conformational Changes of Simple Helix Bundles. J. Comput. Biol. 13(1): 21-42 (2006) - [j12]Tamar Schlick, Ken A. Dill:
Special Section On Multiscale Modeling In Biology. Multiscale Model. Simul. 5(4): 1174 (2006) - [j11]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): 1214-1226 (2006) - [j10]Bosco K. Ho, Ken A. Dill:
Folding Very Short Peptides Using Molecular Dynamics. PLoS Comput. Biol. 2(4) (2006) - [j9]Bosco K. Ho, Ken A. Dill:
Correction: Folding Very Short Peptides Using Molecular Dynamics. PLoS Comput. Biol. 2(5) (2006) - 2005
- [j8]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): 1663-1665 (2005) - 2004
- [j7]Evangelos A. Coutsias, Chaok Seok, Matthew P. Jacobson, Ken A. Dill:
A kinematic view of loop closure. J. Comput. Chem. 25(4): 510-528 (2004) - [j6]Evangelos A. Coutsias, Chaok Seok, Ken A. Dill:
Using quaternions to calculate RMSD. J. Comput. Chem. 25(15): 1849-1857 (2004) - 2003
- [j5]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): 239-255 (2003) - [j4]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): 89-97 (2003) - 2002
- [j3]Keith D. Ball, Burak Erman, Ken A. Dill:
The elastic net algorithm and protein structure prediction. J. Comput. Chem. 23(1): 77-83 (2002) - 1999
- [j2]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): 1527-1532 (1999) - 1997
- [j1]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): 227-239 (1997)
Conference and Workshop Papers
- 2006
- [c5]Julia Hockenmaier, Aravind K. Joshi, Ken A. Dill:
Protein folding and chart parsing. EMNLP 2006: 293-300 - 2003
- [c4]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: 240-251 - 2002
- [c3]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: 2-11 - 1998
- [c2]Philip F. LoCascio, Kaizhi Yue, Peter Cummings, Ken A. Dill:
The Large Scale Parallelization of a Conformational 3D Protein Structure Prediction Application. SC 1998: 40 - 1997
- [c1]Ken A. Dill, Andrew T. Phillips, J. Ben Rosen:
Protein structure prediction and potential energy landscape analysis using continuous global minimization. RECOMB 1997: 109-117
Informal and Other Publications
- 2017
- [i3]Michael J. Hazoglu, Vivek Kulkarni, Steven Skiena, Ken A. Dill:
Citation histories of papers: sometimes the rich get richer, sometimes they don't. CoRR abs/1703.04746 (2017) - 2011
- [i2]G. J. Peterson, Ken A. Dill:
Power-law distribution functions derived from maximum entropy and a symmetry relationship. CoRR abs/1112.5906 (2011) - 2010
- [i1]G. J. Peterson, Steve Pressé, Ken A. Dill:
Nonuniversal power law scaling in the probability distribution of scientific citations. CoRR abs/1009.0574 (2010)
Coauthor Index
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