Pablo Gainza
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Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
P Gainza, F Sverrisson, F Monti, E Rodola, D Boscaini, MM Bronstein, ...
Nature Methods 17 (2), 184-192, 2020
OSPREY: protein design with ensembles, flexibility, and provable algorithms
P Gainza*, KE Roberts*, I Georgiev, RH Lilien, DA Keedy, CY Chen, ...
Methods in enzymology 523, 87-107, 2013
Protein design using continuous rotamers
P Gainza*, KE Roberts*, BR Donald
PLoS Comput Biol 8 (1), e1002335, 2012
Optimization of therapeutic antibodies by predicting antigen specificity from antibody sequence via deep learning
DM Mason, S Friedensohn, CR Weber, C Jordi, B Wagner, SM Meng, ...
Nature Biomedical Engineering 5 (6), 600-612, 2021
A computationally designed chimeric antigen receptor provides a small-molecule safety switch for T-cell therapy
G Giordano-Attianese*, P Gainza*, E Gray-Gaillard*, E Cribioli, S Shui, ...
Nature Biotechnology 38 (4), 426-432, 2020
Algorithms for protein design
P Gainza, HM Nisonoff, BR Donald
Current opinion in structural biology 39, 16-26, 2016
Protein design algorithms predict viable resistance to an experimental antifolate
SM Reeve*, P Gainza*, KM Frey, I Georgiev, BR Donald, AC Anderson
Proceedings of the National Academy of Sciences 112 (3), 749-754, 2015
Deep learning enables therapeutic antibody optimization in mammalian cells by deciphering high-dimensional protein sequence space
DM Mason, S Friedensohn, CR Weber, C Jordi, B Wagner, S Meng, ...
BioRxiv, 617860, 2019
Osprey 3.0: open‐source protein redesign for you, with powerful new features
MA Hallen, JW Martin, A Ojewole, JD Jou, AU Lowegard, MS Frenkel, ...
Journal of computational chemistry 39 (30), 2494-2507, 2018
Computational protein design—the next generation tool to expand synthetic biology applications
P Gainza-Cirauqui, BE Correia
Current opinion in biotechnology 52, 145-152, 2018
Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen
F Sesterhenn, M Galloux, SS Vollers, L Csepregi, C Yang, D Descamps, ...
PLoS biology 17 (2), e3000164, 2019
Compact representation of continuous energy surfaces for more efficient protein design
MA Hallen, P Gainza, BR Donald
Journal of chemical theory and computation 11 (5), 2292-2306, 2015
Fast gap‐free enumeration of conformations and sequences for protein design
KE Roberts*, P Gainza*, MA Hallen, BR Donald
Proteins: Structure, Function, and Bioinformatics 83 (10), 1859-1877, 2015
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, ...
Nature Communications 12, 5754, 2021
OSPREY predicts resistance mutations using positive and negative computational protein design
A Ojewole, A Lowegard, P Gainza, SM Reeve, I Georgiev, AC Anderson, ...
Computational Protein Design, 291-306, 2017
OSPREY (Open Source Protein Redesign for You) user manual
I Georgiev, KE Roberts, P Gainza, MA Hallen, BR Donald
De novo design of site-specific protein interactions with learned surface fingerprints
P Gainza*, S Wehrle*, A Van Hall-Beauvais*, A Marchand*, A Scheck*, ...
bioRxiv, 2022
Chiral evasion and stereospecific antifolate resistance in Staphylococcus aureus
S Wang, SM Reeve, GT Holt, AA Ojewole, MS Frenkel, P Gainza, ...
PLoS Computational Biology 18 (2), e1009855, 2022
Computational Protein Design with Ensembles, Flexibility and Mathematical Guarantees, and its Application to Drug Resistance Prediction, and Antibody Design
P Gainza Cirauqui
Rational design of chemically controlled antibodies and protein therapeutics
A Marchand, L Bonati, S Shui, L Scheller, P Gainza, S Rosset, ...
bioRxiv, 2022.12. 22.521584, 2022
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