Author

P. Gainza

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Biochemistry· 3 Bioengineering· 2 Immunology· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 5 Research Focus:drug response / drug discovery· 4 Research Focus:protein design· 3 Assay:protein structure· 3 Organism:human· 2 Assay:proteomics· 2 Approach:statistical model· 2 Organism:bacteria (other)· 1

Frequent Co-Authors

S. Georgeon· 4 shared S. Rosset· 4 shared A. Marchand· 3 shared B. Correia· 3 shared L. Scheller· 3 shared B. E. Correia· 2 shared C. Yang· 2 shared M. Bronstein· 2 shared

Activity by Year

2018-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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4 shared papersBiochemistry

S. Georgeon

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Author profile →

6 papers

Recent·Most cited

Targeting protein-ligand neosurfaces using a generalizable deep learning approach

A. Marchand, S. Buckley, A. Schneuing, M. Pacesa, P. Gainza, E. Elizarova, R. M. Neeser, P.-W. Lee, L. Reymond, M. Elia, L. Scheller, S. Georgeon, J. Schmidt, P. Schwaller, S. J. Maerkl, , B. E. Correia

This paper designs proteins that target neosurfaces from protein-ligand complexes using a deep learning approach, validated experimentally against three drug-bound protein complexes.

bioRxiv · Mar 25, 2024 · PreprintBiochemistry

Rational design of chemically controlled antibodies and protein therapeutics

A. Marchand, L. Bonati, S. Shui, L. Scheller, P. Gainza, S. Rosset, S. Georgeon, L. Tang, B. Correia

This study designs and tests small molecule-controlled switchable protein therapeutics by optimizing protein interactions and demonstrating in vitro and in vivo controllability with Venetoclax.

bioRxiv · Dec 22, 2022 · PreprintBioengineering

De novo design of site-specific protein interactions with learned surface fingerprints

P. Gainza, S. Wehrle, A. Van Hall-Beauvais, A. Marchand, A. Scheck, Z. Harteveld, D. Ni, S. Tan, F. Sverrisson, C. Goverde, P. Turelli, C. Raclot, A. Teslenko, M. Pacesa, S. Rosset, , B. E. Correia

This paper designs novel protein interactions using geometric deep learning to generate surface fingerprints, achieving nanomolar affinity for four targets through computational and experimental methods.

bioRxiv · Jun 16, 2022 · PreprintBioengineering

A rational blueprint for the design of chemically-controlled protein switches

S. Shui, P. Gainza, L. Scheller, C. Yang, Y. Kurumida, S. Georgeon, S. Rosset, B. Correia

This paper presents a computational strategy to design chemically-controlled protein switches using drug-inhibited interactions, expanding chemical space for synthetic circuits in mammalian cells.

bioRxiv · Jan 21, 2021Biochemistry

Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus

S. Wang, S. M. Reeve, A. A. Ojewole, M. S. Frenkel, G. T. Holt, P. Gainza, S. Keshipeddy, V. G. Fowler, D. L. Wright, B. R. Donald

The paper investigates how a mutation in Staphylococcus aureus dihydrofolate reductase affects antifolate resistance and NADPH isomerism through chiral evasion mechanisms.

bioRxiv · Jul 28, 2020Biochemistry

Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen

F. Sesterhenn, M. Galloux, S. S. Vollers, L. Csepregi, C. Yang, D. Descamps, J. Bonet, S. Friedensohn, P. Gainza, P. Corthesy, M. Chen, S. Rosset, M.-A. Rameix-Welti, J.-F. Eleouet, S. T. Reddy, , B. Correia

This study demonstrates that a computationally designed epitope-focused immunogen enhances subdominant neutralizing antibody responses against RSV.

bioRxiv · Nov 22, 2018Immunology