Cecilia Clementi

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 40

Top Topics

Single Molecule

Molecular Dynamics

Top Venues

Journal of chemical theory and computation

The Journal of chemical physics

Nature communications

The journal of physical chemistry letters

This page only lists publications with an associated author ORCID identifier.

Publications

Patrick Bryant, Atharva Kelkar, Andrea Guljas, Cecilia Clementi, Frank Noé
Structure prediction of protein-ligand complexes from sequence information with Umol. Nature communications 15 (1) (2024)
Patrick Bryant, Atharva Kelkar, Andrea Guljas, Cecilia Clementi, Frank Noé
Structure prediction of protein-ligand complexes from sequence information with Umol. Nature communications 15 (1) (2024)
Patrick Bryant, Atharva Kelkar, Andrea Guljas, Cecilia Clementi, Frank Noé
Structure prediction of protein-ligand complexes from sequence information with Umol. Nature communications 15 (1) (2024)
Patrick Bryant, Atharva Kelkar, Andrea Guljas, Cecilia Clementi, Frank Noé
Structure prediction of protein-ligand complexes from sequence information with Umol. Nature communications 15 (1) (2024)
Andreas Krämer, Aleksander E P Durumeric, Nicholas E Charron, Yaoyi Chen, Cecilia Clementi, Frank Noé
Statistically Optimal Force Aggregation for Coarse-Graining Molecular Dynamics. The journal of physical chemistry letters (2023)
Maciej Majewski, Adrià Pérez, Philipp Thölke, Stefan Doerr, Nicholas E Charron, Toni Giorgino, Brooke E Husic, Cecilia Clementi, Frank Noé, Gianni De Fabritiis
Machine learning coarse-grained potentials of protein thermodynamics. Nature communications 14 (1) (2023)
Andreas Krämer, Aleksander E P Durumeric, Nicholas E Charron, Yaoyi Chen, Cecilia Clementi, Frank Noé
Statistically Optimal Force Aggregation for Coarse-Graining Molecular Dynamics. The journal of physical chemistry letters 14 (17) (2023)
Andreas Krämer, Aleksander E P Durumeric, Nicholas E Charron, Yaoyi Chen, Cecilia Clementi, Frank Noé
Statistically Optimal Force Aggregation for Coarse-Graining Molecular Dynamics. The journal of physical chemistry letters (2023)
Jonas Köhler, Yaoyi Chen, Andreas Krämer, Cecilia Clementi, Frank Noé
Flow-Matching: Efficient Coarse-Graining of Molecular Dynamics without Forces. Journal of chemical theory and computation (2023)
Marloes Arts, Victor Garcia Satorras, Chin-Wei Huang, Daniel Zügner, Marco Federici, Cecilia Clementi, Frank Noé, Robert Pinsler, Rianne van den Berg
Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics. Journal of chemical theory and computation (2023)
Anja Conev, Mauricio Menagatti Rigo, Didier Devaurs, André Faustino Fonseca, Hussain Kalavadwala, Martiela Vaz de Freitas, Cecilia Clementi, Geancarlo Zanatta, Dinler Amaral Antunes, Lydia E Kavraki
EnGens: a computational framework for generation and analysis of representative protein conformational ensembles. Briefings in bioinformatics (2023)
Anja Conev, Mauricio Menagatti Rigo, Didier Devaurs, André Faustino Fonseca, Hussain Kalavadwala, Martiela Vaz de Freitas, Cecilia Clementi, Geancarlo Zanatta, Dinler Amaral Antunes, Lydia E Kavraki
EnGens: a computational framework for generation and analysis of representative protein conformational ensembles. bioRxiv : the preprint server for biology (2023)
Wangfei Yang, Clark Templeton, David Rosenberger, Andreas Bittracher, Feliks Nüske, Frank Noé, Cecilia Clementi
Slicing and Dicing: Optimal Coarse-Grained Representation to Preserve Molecular Kinetics. ACS central science 9 (2) (2023)
Wangfei Yang, Clark Templeton, David Rosenberger, Andreas Bittracher, Feliks Nüske, Frank Noé, Cecilia Clementi
Slicing and Dicing: Optimal Coarse-Grained Representation to Preserve Molecular Kinetics. ACS central science 9 (2) (2023)
Anja Conev, Mauricio Menagatti Rigo, Didier Devaurs, André Faustino Fonseca, Hussain Kalavadwala, Martiela Vaz de Freitas, Cecilia Clementi, Geancarlo Zanatta, Dinler Amaral Antunes, Lydia E Kavraki
EnGens: a computational framework for generation and analysis of representative protein conformational ensembles. bioRxiv : the preprint server for biology (2023)
Iryna Zaporozhets, Cecilia Clementi
Multibody Terms in Protein Coarse-Grained Models: A Top-Down Perspective. The journal of physical chemistry. B (2023)
Andreas Krämer, Aleksander E P Durumeric, Nicholas E Charron, Yaoyi Chen, Cecilia Clementi, Frank Noé
Statistically Optimal Force Aggregation for Coarse-Graining Molecular Dynamics. The journal of physical chemistry letters (2023)
Andreas Krämer, Aleksander E P Durumeric, Nicholas E Charron, Yaoyi Chen, Cecilia Clementi, Frank Noé
Statistically Optimal Force Aggregation for Coarse-Graining Molecular Dynamics. The journal of physical chemistry letters 14 (17) (2023)
Jonas Köhler, Yaoyi Chen, Andreas Krämer, Cecilia Clementi, Frank Noé
Flow-Matching: Efficient Coarse-Graining of Molecular Dynamics without Forces. Journal of chemical theory and computation 19 (3) (2023)
Anja Conev, Mauricio Menagatti Rigo, Didier Devaurs, André Faustino Fonseca, Hussain Kalavadwala, Martiela Vaz de Freitas, Cecilia Clementi, Geancarlo Zanatta, Dinler Amaral Antunes, Lydia E Kavraki
EnGens: a computational framework for generation and analysis of representative protein conformational ensembles. bioRxiv : the preprint server for biology (2023)
Andreas Mardt, Tim Hempel, Cecilia Clementi, Frank Noé
Deep learning to decompose macromolecules into independent Markovian domains. Nature communications 13 (1) (2022)
Michele Invernizzi, Andreas Krämer, Cecilia Clementi, Frank Noé
Skipping the Replica Exchange Ladder with Normalizing Flows. The journal of physical chemistry letters (2022)
Jiang Wang, Stefan Chmiela, Klaus-Robert Müller, Frank Noé, Cecilia Clementi
Ensemble learning of coarse-grained molecular dynamics force fields with a kernel approach. The Journal of chemical physics 152 (19) (2021)
Aldo Glielmo, Brooke E Husic, Alex Rodriguez, Cecilia Clementi, Frank Noé, Alessandro Laio
Unsupervised Learning Methods for Molecular Simulation Data. Chemical reviews 121 (16) (2021)
Stefan Doerr, Maciej Majewski, Adrià Pérez, Andreas Krämer, Cecilia Clementi, Frank Noe, Toni Giorgino, Gianni De Fabritiis
TorchMD: A Deep Learning Framework for Molecular Simulations. Journal of chemical theory and computation 17 (4) (2021)
Jiang Wang, Nicholas E Charron, Brooke E Husic, Simon Olsson, Frank Noé, Cecilia Clementi
Multi-body effects in a coarse-grained protein force field. The Journal of chemical physics 154 (16) (2021)
Yaoyi Chen, Andreas Krämer, Nicholas E Charron, Brooke E Husic, Cecilia Clementi, Frank Noé
Machine learning implicit solvation for molecular dynamics. The Journal of chemical physics 155 (8) (2021)
Cecilia Clementi
Fast track to structural biology. Nature chemistry 13 (11) (2021)
Brooke E Husic, Nicholas E Charron, Dominik Lemm, Jiang Wang, Adrià Pérez, Maciej Majewski, Andreas Krämer, Yaoyi Chen, Simon Olsson, Gianni de Fabritiis, Frank Noé, Cecilia Clementi
Coarse graining molecular dynamics with graph neural networks. The Journal of chemical physics 153 (19) (2020)
Jayvee R Abella, Dinler Amaral Antunes, Kyle R Jackson, Gregory Lizée, Cecilia Clementi, Lydia E Kavraki
Markov state modeling reveals alternative unbinding pathways for peptide-MHC complexes. Proceedings of the National Academy of Sciences of the United States of America 117 (48) (2020)
Eugen Hruska, Vivekanandan Balasubramanian, Hyungro Lee, Shantenu Jha, Cecilia Clementi
Extensible and Scalable Adaptive Sampling on Supercomputers. Journal of chemical theory and computation 16 (12) (2020)
Martin Lehmann, Ilya Lukonin, Frank Noé, Jan Schmoranzer, Cecilia Clementi, Dinah Loerke, Volker Haucke
Nanoscale coupling of endocytic pit growth and stability. Science advances 5 (11) (2019)
Justin Chen, Nicholas P Schafer, Peter G Wolynes, Cecilia Clementi
Localizing Frustration in Proteins Using All-Atom Energy Functions. The journal of physical chemistry. B 123 (21) (2019)
Jayvee R Abella, Dinler Amaral Antunes, Cecilia Clementi, Lydia E Kavraki
APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations. Molecules (Basel, Switzerland) 24 (5) (2019)
Eugen Hruska, Jayvee R Abella, Feliks Nüske, Lydia E Kavraki, Cecilia Clementi
Quantitative comparison of adaptive sampling methods for protein dynamics. The Journal of chemical physics 149 (24) (2019)
Fernando Miguel Yrazu, Giovanni Pinamonti, Cecilia Clementi
The Effect of Electrostatic Interactions on the Folding Kinetics of a 3-α-Helical Bundle Protein Family. The journal of physical chemistry. B 122 (49) (2018)
Florian Litzinger, Lorenzo Boninsegna, Hao Wu, Feliks Nüske, Raajen Patel, Richard Baraniuk, Frank Noé, Cecilia Clementi
Rapid Calculation of Molecular Kinetics Using Compressed Sensing. Journal of chemical theory and computation 14 (5) (2018)
Justin Chen, Jiming Chen, Giovanni Pinamonti, Cecilia Clementi
Learning Effective Molecular Models from Experimental Observables. Journal of chemical theory and computation 14 (7) (2018)
Anna I Krylov, Theresa L Windus, Taylor Barnes, Eliseo Marin-Rimoldi, Jessica A Nash, Benjamin Pritchard, Daniel G A Smith, Doaa Altarawy, Paul Saxe, Cecilia Clementi, T Daniel Crawford, Robert J Harrison, Shantenu Jha, Vijay S Pande, Teresa Head-Gordon
Perspective: Computational chemistry software and its advancement as illustrated through three grand challenge cases for molecular science. The Journal of chemical physics 149 (18) (2018)
Lorenzo Boninsegna, Ralf Banisch, Cecilia Clementi
A Data-Driven Perspective on the Hierarchical Assembly of Molecular Structures. Journal of chemical theory and computation 14 (1) (2017)