Protein structure prediction and potential energy landscape analysis using continuous global minimization. - Ken A. Dill; Andrew T. Phillips; J. Ben Rosen (RECOMB, 1997)

Protein Structure and Energy Landscape Dependence on Sequence Using a Continuous Energy Function. - Ken A. Dill; Andrew T. Phillips; J. Ben Rosen (J. Comput. Biol., 1997)

The Large Scale Parallelization of a Conformational 3D Protein Structure Prediction Application. - Philip F. LoCascio; Kaizhi Yue; Peter Cummings; Ken A. Dill (SC, 1998)

Comparing search strategies for finding global optima on energy landscapes. - K. W. Foreman; Andrew T. Phillips; J. Ben Rosen; Ken A. Dill (J. Comput. Chem., 1999)

The elastic net algorithm and protein structure prediction. - Keith D. Ball; Burak Erman; Ken A. Dill (J. Comput. Chem., 2002)

A Path Planning-Based Study of Protein Folding with a Case Study of Hairpin Formation in Protein G and L. - Guang Song; Shawna L. Thomas; Ken A. Dill; J. Martin Scholtz; Nancy M. Amato (Pacific Symposium on Biocomputing, 2003)

Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures. - Nancy M. Amato; Ken A. Dill; Guang Song (J. Comput. Biol., 2003)

MOPED: Method for optimizing physical energy parameters using decoys. - Chaok Seok; J. Ben Rosen; John D. Chodera; Ken A. Dill (J. Comput. Chem., 2003)

Using quaternions to calculate RMSD. - Evangelos A. Coutsias; Chaok Seok; Ken A. Dill (J. Comput. Chem., 2004)

A kinematic view of loop closure. - Evangelos A. Coutsias; Chaok Seok; Matthew P. Jacobson; Ken A. Dill (J. Comput. Chem., 2004)

Rotational superposition and least squares: The SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller. - Evangelos A. Coutsias; Chaok Seok; Ken A. Dill (J. Comput. Chem., 2005)

Protein folding and chart parsing. - Julia Hockenmaier; Aravind K. Joshi; Ken A. Dill (EMNLP, 2006)

A Grammatical Theory for the Conformational Changes of Simple Helix Bundles. - David Chiang 001; Aravind K. Joshi; Ken A. Dill (J. Comput. Biol., 2006)

Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations. - John D. Chodera; William C. Swope; Jed W. Pitera; Ken A. Dill (Multiscale Model. Simul., 2006)

Special Section On Multiscale Modeling In Biology. - Tamar Schlick; Ken A. Dill (Multiscale Model. Simul., 2006)

Folding Very Short Peptides Using Molecular Dynamics. - Bosco K. Ho; Ken A. Dill (PLoS Comput. Biol., 2006)

Correction: Folding Very Short Peptides Using Molecular Dynamics. - Bosco K. Ho; Ken A. Dill (PLoS Comput. Biol., 2006)

Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments. - Vincent A. Voelz; M. Scott Shell; Ken A. Dill (PLoS Comput. Biol., 2009)

Nonuniversal power law scaling in the probability distribution of scientific citations - G. J. Peterson; Steve Pressé; Ken A. Dill (CoRR, 2010)

Power-law distribution functions derived from maximum entropy and a symmetry relationship - G. J. Peterson; Ken A. Dill (CoRR, 2011)

Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test. - Charles W. Kehoe; Christopher J. Fennell; Ken A. Dill (J. Comput. Aided Mol. Des., 2012)

Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge. - Libo Li; Ken A. Dill; Christopher J. Fennell (J. Comput. Aided Mol. Des., 2014)

Reply to C. Tsallis' "Conceptual Inadequacy of the Shore and Johnson Axioms for Wide Classes of Complex Systems". - Steve Pressé; Kingshuk Ghosh; Julian Lee; Ken A. Dill (Entropy, 2015)

Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules. - Emiliano Brini; S. Shanaka Paranahewage; Christopher J. Fennell; Ken A. Dill (J. Comput. Aided Mol. Des., 2016)

Citation histories of papers: sometimes the rich get richer, sometimes they don't. - Michael J. Hazoglu; Vivek Kulkarni; Steven Skiena; Ken A. Dill (CoRR, 2017)

Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge. - Mikhail Ignatov; Cong Liu 031; Andrey Alekseenko; Zhuyezi Sun; Dzmitry Padhorny; Sergei Kotelnikov; Andrey M. Kazennov; Ivan Grebenkin; Yaroslav Kholodov; Istvan Kolosvari; Alberto Pérez; Ken A. Dill; et al. (J. Comput. Aided Mol. Des., 2019)

Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4. - Sergei Kotelnikov; Andrey Alekseenko; Cong Liu 031; Mikhail Ignatov; Dzmitry Padhorny; Emiliano Brini; Mark Lukin; Evangelos A. Coutsias; Ken A. Dill; Dima Kozakov (J. Comput. Aided Mol. Des., 2020)

Proteostasis is adaptive: Balancing chaperone holdases against foldases. - Adam M. R. de Graff; David E. Mosedale; Tilly Sharp; Ken A. Dill; David J. Grainger (PLoS Comput. Biol., 2020)

Inferring a network from dynamical signals at its nodes. - Corey Weistuch; Luca Agozzino; Lilianne R. Mujica-Parodi; Ken A. Dill (PLoS Comput. Biol., 2020)

MELD-Bracket Ranks Binding Affinities of Diverse Sets of Ligands. - Sridip Parui; James C. Robertson; Sandeep Somani; Gary Tresadern; Cong Liu 031; Ken A. Dill (J. Chem. Inf. Model., 2023)

MELD in Action: Harnessing Data to Accelerate Molecular Dynamics. - Jokent T. Gaza; Emiliano Brini; Justin L. Maccallum; Ken A. Dill; Alberto Pérez (J. Chem. Inf. Model., 2025)