Topological and energetic factors: what determines the structural details of the transition state ensemble and “en-route” intermediates for protein folding? An investigation … C Clementi, H Nymeyer, JN Onuchic Journal of molecular biology 298 (5), 937-953, 2000 | 1383 | 2000 |
Machine learning for molecular simulation F Noé, A Tkatchenko, KR Müller, C Clementi Annual review of physical chemistry 71, 361-390, 2020 | 688 | 2020 |
Machine learning of coarse-grained molecular dynamics force fields J Wang, S Olsson, C Wehmeyer, A Pérez, NE Charron, G de Fabritiis, ... ACS Central Science, 2019 | 429 | 2019 |
Coarse-grained models of protein folding: toy models or predictive tools? C Clementi Current opinion in structural biology 18 (1), 10-15, 2008 | 393 | 2008 |
Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction P Das, M Moll, H Stamati, LE Kavraki, C Clementi Proceedings of the National Academy of Sciences 103 (26), 9885-9890, 2006 | 371 | 2006 |
AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing A Davtyan, NP Schafer, W Zheng, C Clementi, PG Wolynes, GA Papoian The Journal of Physical Chemistry B 116 (29), 8494-8503, 2012 | 312 | 2012 |
Determination of reaction coordinates via locally scaled diffusion map MA Rohrdanz, W Zheng, M Maggioni, C Clementi The Journal of chemical physics 134 (12), 2011 | 312 | 2011 |
Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates LL Chavez, JN Onuchic, C Clementi Journal of the American Chemical Society 126 (27), 8426-8432, 2004 | 271 | 2004 |
Unsupervised learning methods for molecular simulation data A Glielmo, BE Husic, A Rodriguez, C Clementi, F Noé, A Laio Chemical Reviews 121 (16), 9722-9758, 2021 | 248 | 2021 |
How native-state topology affects the folding of dihydrofolate reductase and interleukin-1β C Clementi, PA Jennings, JN Onuchic Proceedings of the National Academy of Sciences 97 (11), 5871-5876, 2000 | 247 | 2000 |
Sparse learning of stochastic dynamic equations L Boninsegna, F Nüske, C Clementi J. Chem. Phys. 148, 241723, 2018 | 245 | 2018 |
Discovering mountain passes via torchlight: Methods for the definition of reaction coordinates and pathways in complex macromolecular reactions MA Rohrdanz, W Zheng, C Clementi Annual review of physical chemistry 64, 295-316, 2013 | 231 | 2013 |
Data-driven approximation of the Koopman generator: Model reduction, system identification, and control S Klus, F Nüske, S Peitz, JH Niemann, C Clementi, C Schütte Physica D: Nonlinear Phenomena 406, 132416, 2020 | 221 | 2020 |
Kinetic distance and kinetic maps from molecular dynamics simulation F Noé, C Clementi Journal of Chemical Theory and Computation 11 (10), 5002–5011, 2015 | 219 | 2015 |
Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L C Clementi, AE Garcıa, JN Onuchic Journal of molecular biology 326 (3), 933-954, 2003 | 217 | 2003 |
The effects of nonnative interactions on protein folding rates: Theory and simulation C Clementi, SS Plotkin Protein Science 13 (7), 1750-1766, 2004 | 192 | 2004 |
Riemannian theory of Hamiltonian chaos and Lyapunov exponents L Casetti, C Clementi, M Pettini Physical Review E 54 (6), 5969, 1996 | 192 | 1996 |
Geometry of dynamics, Lyapunov exponents, and phase transitions L Caiani, L Casetti, C Clementi, M Pettini Physical review letters 79 (22), 4361, 1997 | 176 | 1997 |
Jagged–Delta asymmetry in Notch signaling can give rise to a Sender/Receiver hybrid phenotype M Boareto, MK Jolly, M Lu, JN Onuchic, C Clementi, E Ben-Jacob Proceedings of the National Academy of Sciences 112 (5), E402-E409, 2015 | 163 | 2015 |
Dynamics of polymer translocation through nanopores: theory meets experiment S Matysiak, A Montesi, M Pasquali, AB Kolomeisky, C Clementi Physical review letters 96 (11), 118103, 2006 | 163 | 2006 |