Author

Francesco Paesani

San Diego Supercomputer CenterORCID 0000-0002-4451-1203Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Biophysics· 2 Bioengineering· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Assay:protein structure· 2 Research Focus:benchmarking· 1 Approach:machine learning (classical)· 1 Research Focus:protein design· 1 Assay:protein sequence· 1 Research Focus:protein structure prediction· 1 Approach:statistical model· 1

Frequent Co-Authors

Cianna N. CaliaiD· 3 shared Adaptyv Competition Organizers· 1 shared Ahmad Zaman Qamar· 1 shared Alexander Naka· 1 shared Anthony GitteriD· 1 shared Arthur J. AltunciD· 1 shared Benjamin O. Alvarado· 1 shared Bruno E. CorreiaiD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 31 mutual co-author links

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3 shared papersBiophysics

Cianna N. CaliaORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

Computational Redesign of an Antifreeze Protein Using Deep Learning

Cianna N. Calia, Arthur J. Altunc, Rosemary J. Eufemio, Benjamin O. Alvarado, Jake D. Huynh, Eunkeu Oh, Michael D. Burkart, Konrad Meister, Francesco Paesani

This study uses deep learning to redesign an antifreeze protein, identifying variants with improved properties but not surpassing wild-type activity.

bioRxiv · Jun 24, 2026 · PreprintBiophysics

Computational Analysis of Threonine Ladders on Distinct Beta-Solenoid Scaffolds, with Implications for the Design of Novel Antifreeze Proteins

Cianna N. Calia, Francesco Paesani

The paper investigates how beta-solenoid scaffolds affect threonine ladder structure and ice-binding properties, suggesting scaffold-specific effects on antifreeze protein design.

The Journal of Physical Chemistry B · Sep 3, 2025Peer-reviewedBiophysics

Crowdsourced Protein Design: Lessons From the Adaptyv EGFR Binder Competition

Tudor‐Stefan Cotet, Igor Krawczuk, Filippo Stocco, Noelia Ferruz, Anthony Gitter, Yoichi Kurumida, Lucas de Almeida Machado, Francesco Paesani, Cianna N. Calia, Chance A. Challacombe, Nikhil Haas, Ahmad Zaman Qamar, Bruno E. Correia, Martin Pačesa, Lennart Nickel, , Adaptyv Competition Organizers

The paper analyzes a crowdsourced protein design competition, showing participants designed EGFR binders with varying affinities and highlighting challenges in benchmarking and experimental design.

bioRxiv · Apr 17, 2025 · PreprintBioengineering