Cecilia Clementi Research Group Publications
last updated on March 07, 2008
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Elsevier
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| Author(s): |
Clementi, C. |
| Title: |
Coarse-grained models of protein folding: Toy-models or predictive tools? |
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Curr. Opin. Struct. Biol. 2008, vol.18(1), pp. 10-15 |
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Elsevier
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| Author(s): |
Matysiak, S. & Clementi, C. |
| Title: |
Mapping folding energy landscapes with theory and experiment |
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Arch. Biochem. Biophys. 2008, vol.469(1), 29-33 |
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local
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| Author(s): |
Matysiak, S., Clementi, C., Praprotnik, M., Kremer, K. & Delle Site, L. |
| Title: |
Modeling Diffusive Dynamics in Adaptive Resolution Simulation of Liquid Water |
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J. Chem. Phys. 2008, vol.128, 024503 |
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Protein Science
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| Author(s): |
Shehu, A., Kavraki, L.E. & Clementi, C. |
| Title: |
Unfolding the Fold of Cyclic Cysteine-rich Peptides |
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Protein Science 2008, vol.17, pp. 482-493 |
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Algorithmica
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| Author(s): |
Shehu, A., Clementi, C. & Kavraki, L.E. |
| Title: |
Sampling Conformational Space to Model
Equilibrium Fluctuations in Proteins |
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Algorithmica 2007, vol. 48(4), pp 303-327 |
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iop
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| Author(s): |
Praprotnik, M., Matysiak, S., Delle Site, L. Kremer, K., & Clementi, C. |
| Title: |
Adaptive resolution simulation of liquid water |
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J. Phys.: Condens. Matter, 2007, vol.19(29), 292201 |
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aps
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| Author(s): |
Mossa, A. & Clementi, C. |
| Title: |
Supersymmetric Langevin equation to explore free energy landscapes |
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Phys. Rev. E, 2007, vol.75, 046707 |
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Proteins
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| Author(s): |
Heath, A.P., Kavraki, L.E. & Clementi, C. |
| Title: |
From Coarse-Grain to All-Atom: Toward
Multiscale Analysis of Protein Landscapes |
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Proteins, 2007, vol.68(3), pp 646-661 (cover article) |
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Proteins
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| Author(s): |
Plaku, E., Stamati, H., Clementi, C. & Kavraki, L.E. |
| Title: |
Fast and Reliable Analysis of Molecular Motion Using
Proximity Relations and Dimensionality Reduction |
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Proteins, 2007, vol. 67(4), pp 897-907 |
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Biophysical Journal
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| Author(s): |
Shehu, A., Kavraki, L.E. & Clementi, C. |
| Title: |
On the Characterization of Protein Native State Ensembles |
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Biophysical Journal, 2007, vol. 92, pp 1503-1511 |
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Proteins
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| Author(s): |
Shehu, A., Clementi, C. & Kavraki, L.E. |
| Title: |
Modeling Protein Conformational Ensembles: From Missing Loops to
Equilibrium Fluctuations |
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Proteins 2006, vol. 65(1), pp 164-179 |
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JMB
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| Author(s): |
Matysiak, S. & Clementi, C. |
| Title: |
Minimalist protein model as a diagnostic tool for misfolding and aggregation |
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J. Mol. Biol. 2006, vol. 363(1), pp 297-308 |
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P.N.A.S.
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| Author(s): |
Das, P., Moll, M., Stamati, H., Kavraki, L.E. & Clementi, C. |
| Title: |
Low-dimensional, free-energy landscapes
of protein-folding reactions by nonlinear
dimensionality reduction |
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P.N.A.S. 2006, vol. 103(26), pp 9885-9890 |
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PRL
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| Author(s): |
Matysiak, S., Montesi, A., Pasquali, M., Kolomeisky, A.B. & Clementi, C. |
| Title: |
Dynamics of Polymer Translocation through Nanopores: Theory Meets Experiment |
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Phys. Rev. Lett. 2006, vol. 96(11), 118103 |
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aps
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| Author(s): |
Mossa, A., Pettini, M. & Clementi, C. |
| Title: |
Hamiltonian dynamics of homopolymer chain models |
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Phys. Rev. E, 2006, vol.74, 041805 |
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P.N.A.S.
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| Author(s): |
Das, P., Wilson, C.J., Fossati, G.,
Wittung-Stafshede, P., Matthews, K.S. & Clementi, C. |
| Title: |
Characterization of the folding landscape of monomeric lactose
repressor: Quantitative comparison of theory and experiment |
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P.N.A.S. 2005, vol. 102(41), pp 14569-14574 |
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P.N.A.S.
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| Author(s): |
Wilson,C.J., Das, P., Clementi, C., Matthews, K.S. &
Wittung-Stafshede, P. |
| Title: |
The experimental folding landscape of monomeric
lactose repressor, a large two-domain protein,
involves two kinetic intermediates |
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P.N.A.S. 2005, vol. 102(41), pp 14563-14568 |
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P.N.A.S.
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| Author(s): |
Das, P., Matysiak, S. & Clementi, C. |
| Title: |
Balancing energy and entropy: A minimalist model for the
characterization of protein folding landscapes |
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P.N.A.S. 2005, vol. 102(29), pp 10141-10146 |
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| Author(s): |
Matysiak, S. & Clementi, C. |
| Title: |
Optimal combination of theory and experiment for the
characterization of the protein folding landscape of S6: How far can a
minimalist model go? |
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J. Mol. Biol. 2004, vol. 343(1), pp 235-248 |
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Protein Science
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| Author(s): |
Clementi, C. & Plotkin, S.S. |
| Title: |
The effects of non-native interactions on protein folding
rates: Theory and simulation |
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Protein Science, 2004, vol. 13 (7), pp 1750-1766 |
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JACS
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| Author(s): |
Chavez, L.L., Onuchic, J.N. & Clementi, C. |
| Title: |
Quantifying the roughness on the Free Energy Landscape: Entropic bottlenecks and protein folding rates |
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J. Am. Chem. Soc. 2004 vol. 126(27), pp 8426-8432 |
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| Author(s): |
Clementi, C., Garcia, A., & Onuchic, J.N. |
| Title: |
Interplay among tertiary contacts, secondary structure formation
and side-chain packing in the protein folding mechanism: an all-atom
representation study |
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J.Mol.Biol. 2003, vol. 326, pp 933-954 |
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local
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| Author(s): |
Clementi, C. Pettini, M. |
| Title: |
A geometric interpretation of integrable motions |
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Celest. Mech. & Dyn. Astr. 2002, vol. 84, pp. 263-281 |
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| Author(s): |
Clementi, C., Jennings, P.A. & Onuchic J.N. |
| Title: |
Prediction of folding mechanism for circular-permuted proteins |
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J.Mol.Biol. 2001, vol. 311, pp 879-890 |
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P.N.A.S.
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| Author(s): |
Clementi, C., Jennings, P.A. & Onuchic J.N. |
| Title: |
How native state topology affects the folding of Dihydrofolate
Reductase and Interleukin-1beta |
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P.N.A.S. 2000, vol. 97, pp 5871-5876 |
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| Author(s): |
Clementi, C., Nymeyer, H. & Onuchic J.N. |
| Title: |
Topological and energetic factors: what determines the structural
details of the transition state ensemble and ``on-route"
intermediates for protein folding? An investigation for small
globular proteins |
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J.Mol.Biol. 2000, vol. 298, pp 937-953 |
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PRE
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| Author(s): |
Cerruti-Sola, M., Clementi, C. & Pettini, M. |
| Title: |
Hamiltonian dynamics and geometry of phase transitions in XY models |
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Physical Review E 2000, Vol 61, Iss 5, pp 5171-5190 |
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Proteins - SFG
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| Author(s): |
Clementi, C., Vendruscolo, M., Maritan, A. & Domany, E. |
| Title: |
Folding Lennard-Jones proteins by a contact potential |
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Proteins - Structure Function and Genetics 1999, vol. 37, Iss 4, pp 544-553 |
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P.N.A.S.
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| Author(s): |
Clementi, C., Carloni, P., & Maritan, A. |
| Title: |
Protein design is a key factor for subunit-subunit association |
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P.N.A.S. 1999, vol. 96, Iss 17, pp 9616-9621 |
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J. Chem. Phys.
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| Author(s): |
van Mourik, J., Clementi, C., Maritan, A., Seno, F., & Banavar, J.R. |
| Title: |
Determination of interaction potentials of amino acids from native
protein structures: Tests on simple lattice models |
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Journal of Chemical Physics 1999, vol. 110, Iss 20, pp 10123-10133 |
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PRL
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| Author(s): |
Clementi, C., Maritan, A., & Banavar, J.R. |
| Title: |
Folding, design, and determination of interaction potentials using
off-lattice dynamics of model heteropolymers |
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Physical Review Letters 1998, Vol 81, Iss 15, pp 3287-3290 |
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PRE
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| Author(s): |
Caiani, L., Casetti, L., Clementi, C., Pettini, G., Pettini, M., & Gatto R. |
| Title: |
Geometry of dynamics and phase transitions in classical lattice phi(4) theories |
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Physical Review E 1998, Vol 57, Iss 4, pp 3886-3899 |
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PRL
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| Author(s): |
Caiani, L., Casetti, L., Clementi, C., & Pettini, M. |
| Title: |
Geometry of dynamics, Lyapunov exponents, and phase transitions |
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Physical Review Letters 1997, Vol 79, Iss 22, pp 4361-4364 |
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PRE
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| Author(s): |
Casetti, L., Clementi, C., & Pettini, M. |
| Title: |
Riemannian theory of Hamiltonian chaos and Lyapunov exponents |
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Physical Review E 1996, vol. 54, Iss 6, pp 5969-5984 |
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