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Stamati H, Clementi C, Kavraki LE.  2010.  Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides. Proteins. 78:223-235.
Abstract           Publisher's web site     
Shehu A, Clementi C, Kavraki LE.  2006.  Modeling Protein Conformational Ensembles: From Missing Loops to Equilibrium Fluctuations. Proteins: Structure, Function and Bioinformatics. 65:164-179.
Abstract           Publisher's web site     
Shehu A, Clementi C, Kavraki LE.  2007.  Sampling Conformation Space to Model Equilibrium Fluctuations in Proteins. Algorithmica. 48(4):303-327.
Abstract           Publisher's web site     
Shehu A, Kavraki LE, Clementi C.  2008.  Unfolding the Fold of Cyclic Cysteine-rich Peptides. Protein Science. 17(3):482-493.
Abstract           Publisher's web site     
Shehu A, Kavraki LE, Clementi C.  2007.  On the Characterization of Protein Native State Ensembles. Biophysical Journal. 92:1503-1511.
Abstract           Publisher's web site     
Shehu A, Kavraki LE, Clementi C.  2009.  Multiscale characterization of protein conformational ensembles. Proteins. 76:837-851.
Abstract           Publisher's web site     
P
Plaku E, Stamati H, Clementi C, Kavraki LE.  2007.  Fast and Reliable Analysis of Molecular Motion Using Proximity Relations and Dimensionality Reduction. Proteins: Structure, Function, and Bioinformatics. 67:897--907.
Abstract           Publisher's web site     
H
Heath AP, Kavraki LE, Clementi C.  2007.  From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes. Proteins: Structure, Function and Bioinformatics. 68:646-661.
Abstract           Publisher's web site     
D
Das P, Moll M, Stamati H, Kavraki LE, Clementi C.  2006.  Low-dimensional Free-energy Landscapes of Protein-Folding Reactions by Nonlinear Dimensionality Reduction. Proceedings of the National Academy of Sciences. 103:9885-9890.
Abstract      Preprint PDF     Publisher's web site