Biblio

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2010
Haspel, N, Moll M, Baker ML, Chiu W, Kavraki LE.  2010.  Tracing conformational changes in proteins. BMC Structural Biology. 10:S1.
Abstract      Preprint PDF     Publisher's web site     
2009
Haspel, N, Geisbrecht B, Lambris JD, Kavraki LE.  2009.  Multi-scale Characterization of the Energy Landscape of Proteins with Application to the C3d/Efb-C Complex. Proteins: Structure, function and bioinformatics. 78:1004-1014.
     Publisher's web site     
Haspel, N, Moll M, Baker ML, Chiu W, Kavraki LE.  2009.  Tracing Conformational Changes in Proteins. IEEE Intl. Conf. on Bioinformatics and Biomedicine Workshops (BIBMW).
Abstract      Preprint PDF     Publisher's web site     
2008
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     
2007
Moll, M, Schwarz D, Kavraki LE.  2007.  Roadmap Methods for Protein Folding. Protein Structure Prediction: Methods and Protocols.
Abstract      Preprint PDF     Publisher's web site     
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     
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, Clementi C, Kavraki LE.  2007.  Sampling Conformation Space to Model Equilibrium Fluctuations in Proteins. Algorithmica. 48(4):303-327.
Abstract           Publisher's web site     
2006
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     
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     
2004
Moll, M, Schwarz D, Heath AP, Kavraki LE.  2004.  On Flexible Docking Using Expansive Search.
Abstract      Preprint PDF