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2008
Unfolding the Fold of Cyclic Cysteine-rich Peptides, Shehu A, Kavraki LE, Clementi C , Protein Science, Volume 17, Issue 3, p.482-493, (2008)

2007
Fast and Reliable Analysis of Molecular Motion Using Proximity Relations and Dimensionality Reduction, Plaku E, Stamati H, Clementi C, Kavraki LE , Proteins: Structure, Function, and Bioinformatics, Volume 67, Number 4, p.897--907, (2007)

On the Characterization of Protein Native State Ensembles, Shehu A, Kavraki LE, Clementi C , Biophysical Journal, Volume 92, Number 5, p.1503-1511, (2007)

Roadmap Methods for Protein Folding, Moll M, Schwarz D, Kavraki LE, and Bystroff ZMC , Protein Structure Prediction: Methods and Protocols, Oct., (2007)

Sampling Conformation Space to Model Equilibrium Fluctuations in Proteins, Shehu A, Clementi C, Kavraki LE , Algorithmica, Volume 48, Issue 4, p.303-327, (2007)

2006
Low-dimensional Free-energy Landscapes of Protein-Folding Reactions by Nonlinear Dimensionality Reduction, Das P, Moll M, Stamati H, Kavraki LE, Clementi C , Proceedings of the National Academy of Sciences, June 17, Volume 103, Number 26, p.9885-9890, (2006)

Modeling Protein Conformational Ensembles: From Missing Loops to Equilibrium Fluctuations, Shehu A, Clementi C, Kavraki LE , Proteins: Structure, Function and Bioinformatics, Volume 65, Number 1, p.164-179, (2006)

2004
On Flexible Docking Using Expansive Search, Moll M, Schwarz D, Heath A, Kavraki LE , Number 04-443, Houston, TX, (2004)