Clementi, Cecilia

Scalable emulation of protein equilibrium ensembles with generative deep learning

Lewis, S., Hempel, T., Jiménez-Luna, J., Gastegger, M., Xie, Y., Foong, A. Y. K., Satorras, V. G., Abdin, O., Veeling, B. S., Zaporozhets, I., et al. (2025) · Science

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 390

Scalable emulation of protein equilibrium ensembles with generative deep learning

Lewis, S., Hempel, T., Jiménez Luna, J., Gastegger, M., Xie, Y., Foong, A. Y. K., García Satorras, V., Abdin, O., Veeling, B. S., Zaporozhets, I., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 349

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

Das, P., Moll, M., Stamati, H., Kavraki, L. E., & Clementi, C. (2006) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 331

Determination of reaction coordinates via locally scaled diffusion map

Rohrdanz, M. A., Zheng, W., Maggioni, M., & Clementi, C. (2011) · The Journal of Chemical Physics

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 292

Discovering Mountain Passes via Torchlight: Methods for the Definition of Reaction Coordinates and Pathways in Complex Macromolecular Reactions

Rohrdanz, M. A., Zheng, W., & Clementi, C. (2013) · Annual Review of Physical Chemistry

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 242

TorchMD: A Deep Learning Framework for Molecular Simulations

Doerr, S., Majewski, M., Pérez, A., Krämer, A., Clementi, C., Noe, F., Giorgino, T., & De Fabritiis, G. (2021) · Journal of Chemical Theory and Computation

Machine Learning in Materials ScienceAdvanced Physical and Chemical Molecular Interactions

Cited by 230

Rapid exploration of configuration space with diffusion-map-directed molecular dynamics

Zheng, W., Rohrdanz, M. A., & Clementi, C. (2013) · The Journal of Physical Chemistry B

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 86

Structure prediction of protein-ligand complexes from sequence information with Umol

Bryant, P., Kelkar, A., Guljas, A., Clementi, C., & Noé, F. (2024) · Nature Communications

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 75

Navigating protein landscapes with a machine-learned transferable coarse-grained model

Clementi, C., Charron, N., Musil, F., Guljas, A., Chen, Y., Bonneau, K., Pasos-Trejo, A., Venturin, J., Gusew, D., Zaporozhets, I., et al. (2023) · Nature Chemistry

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 65

Delineation of Folding Pathways of a β-Sheet Miniprotein

Zheng, W., Qi, B., Rohrdanz, M. A., Caflisch, A., Dinner, A. R., & Clementi, C. (2011) · The Journal of Physical Chemistry B

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 39

EnGens: a computational framework for generation and analysis of representative protein conformational ensembles

Conev, A., Rigo, M. M., Devaurs, D., Fonseca, A. F., Kalavadwala, H., de Freitas, M. V., Clementi, C., Zanatta, G., Antunes, D. A., & Kavraki, L. E. (2023) · Briefings in Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 28

EnGens: a computational framework for generation and analysis of representative protein conformational ensembles

Conev, A., Rigo, M. M., Devaurs, D., Fonseca, A. F., Kalavadwala, H., de Freitas, M. V., Clementi, C., Zanatta, G., Antunes, D. A., & Kavraki, L. (2023) · Briefings in Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 28