Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction. - Payel Das; Mark Moll; Hernán Stamati; Lydia E. Kavraki; Cecilia Clementi (Proc. Natl. Acad. Sci. USA, 2006)

Sampling Conformation Space to Model Equilibrium Fluctuations in Proteins. - Amarda Shehu; Cecilia Clementi; Lydia E. Kavraki (Algorithmica, 2007)

Multiscale characterization of macromolecular dynamics: application to photoacitve yellow protein. - Mary A. Rohrdanz; Wenwei Zheng; Bradley Lambeth; Cecilia Clementi (XSEDE, 2013)

Multiscale Approach to the Determination of the Photoactive Yellow Protein Signaling State Ensemble. - Mary A. Rohrdanz; Wenwei Zheng; Bradley Lambeth; Jocelyne Vreede; Cecilia Clementi (PLoS Comput. Biol., 2014)

ExTASY: Scalable and flexible coupling of MD simulations and advanced sampling techniques. - Vivekanandan Balasubramanian; Iain Bethune; Ardita Shkurti; Elena Breitmoser; Eugen Hruska; Cecilia Clementi; Charles A. Laughton; Shantenu Jha (eScience, 2016)

Machine Learning of coarse-grained Molecular Dynamics Force Fields. - Jiang Wang; Christoph Wehmeyer; Frank Noé; Cecilia Clementi (CoRR, 2018)

Porting Adaptive Ensemble Molecular Dynamics Workflows to the Summit Supercomputer. - John R. Ossyra; Ada Sedova; Arnold N. Tharrington; Frank Noé; Cecilia Clementi; Jeremy C. Smith (ISC Workshops, 2019)

Tensor-based EDMD for the Koopman analysis of high-dimensional systems. - Feliks Nüske; Patrick Gelß; Stefan Klus; Cecilia Clementi (CoRR, 2019)

Machine learning for molecular simulation. - Frank Noé; Alexandre Tkatchenko; Klaus-Robert Müller; Cecilia Clementi (CoRR, 2019)

TorchMD: A deep learning framework for molecular simulations. - Stefan Doerr; Maciej Majewski; Adrià Pérez; Andreas Krämer; Cecilia Clementi; Frank Noé; Toni Giorgino; Gianni De Fabritiis (CoRR, 2020)

Spectral Properties of Effective Dynamics from Conditional Expectations. - Feliks Nüske; Péter Koltai; Lorenzo Boninsegna; Cecilia Clementi (Entropy, 2021)

Rapid assessment of T-cell receptor specificity of the immune repertoire. - Xingcheng Lin; Jason T. George; Nicholas P. Schafer; Kevin Ng Chau; Michael E. Birnbaum; Cecilia Clementi; José N. Onuchic; Herbert Levine (Nat. Comput. Sci., 2021)

Force-matching Coarse-Graining without Forces. - Jonas Köhler 001; Yaoyi Chen; Andreas Krämer; Cecilia Clementi; Frank Noé (CoRR, 2022)

Machine Learning Coarse-Grained Potentials of Protein Thermodynamics. - Maciej Majewski; Adrià Pérez; Philipp Thölke; Stefan Doerr; Nicholas E. Charron; Toni Giorgino; Brooke E. Husic; Cecilia Clementi; Frank Noé; Gianni De Fabritiis (CoRR, 2022)

Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics. - Marloes Arts; Victor Garcia Satorras; Chin-Wei Huang; Daniel Zügner; Marco Federici; Cecilia Clementi; Frank Noé; Robert Pinsler; Rianne van den Berg (CoRR, 2023)

EnGens: a computational framework for generation and analysis of representative protein conformational ensembles. - Anja Conev; Maurício Menegatti Rigo; Didier Devaurs; André Faustino Fonseca; Hussain Kalavadwala; Martiela Vaz de Freitas; Cecilia Clementi; Geancarlo Zanatta; Dinler Amaral Antunes; Lydia E. Kavraki (Briefings Bioinform., 2023)