Automated computational design of site-targeted repertoires of camelid antibodies

Informations projet

AutoCAb

N° de convention de subvention: 815379

DOI 10.3030/815379

Projet clôturé

Date de signature de la CE 10 Decembre 2018

Date de début 1 Janvier 2019

Date de fin 31 Decembre 2023

Financé au titre de

• EXCELLENT SCIENCE - European Research Council (ERC)

Coût total € 2 337 500,00

Contribution de l’UE € 2 337 500,00

Coordonné par

WEIZMANN INSTITUTE OF SCIENCE
Israel

Publications

Peer reviewed articles (21)

What Have We Learned from Design of Function in Large Proteins?

Auteurs: Olga Khersonsky; Sarel Fleishman
Publié dans: Biodesign Research, Numéro 1, 2022, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.34133/2022/9787581

Computationally designed dual-color MRI reporters for noninvasive imaging of transgene expression

Auteurs: Hyla Allouche-Arnon, Olga Khersonsky, Nishanth D. Tirukoti, Yoav Peleg, Orly Dym, Shira Albeck, Alexander Brandis, Tevie Mehlman, Liat Avram, Talia Harris, Nirbhay N. Yadav, Sarel J. Fleishman & Amnon Bar-Shir
Publié dans: Nature Biotechnology, 2022, ISSN 1087-0156
Éditeur: Nature Publishing Group
DOI: 10.1038/s41587-021-01162-5

Stable and Functionally Diverse Versatile Peroxidases Designed Directly from Sequences.

Auteurs: Shiran Barber-Zucker; Vladimir Mindel; Eva Garcia-Ruiz; Jonathan J. Weinstein; Miguel Alcalde; Sarel J. Fleishman
Publié dans: Journal of the American Chemical Society, Numéro 1, 2022, ISSN 0002-7863
Éditeur: American Chemical Society
DOI: 10.1021/jacs.1c12433

Reliable energy-based antibody humanization and stabilization

Auteurs: Ariel Tennenhouse; Lev Khmelnitsky; Razi Khalaila; Noa Yeshaya; Ashish Noronha; Moshit Lindzen; Emily Makowski; Ira Zaretsky; Yael Fridmann Sirkis; Yael Galon-Wolfenson; Peter M. Tessier; Jakub Abramson; Yosef Yarden; Deborah Fass; Sarel J. Fleishman
Publié dans: Nature Biomedical Engineering, Numéro 1, 2023, ISSN 2157-846X
Éditeur: Springer Nature
DOI: 10.1038/s41551-023-01079-1

Assessing and enhancing foldability in designed proteins

Auteurs: Dina Listov; Rosalie Lipsh-Sokolik; Stéphane Rosset; Che Yang; Bruno E Correia; Sarel J Fleishman
Publié dans: Protein Science, Numéro 1, 2022, ISSN 1469-896X
Éditeur: Wiley-Blackwell
DOI: 10.1101/2021.11.09.467863

De novo-designed transmembrane domains tune engineered receptor functions

Auteurs: Ashleigh S Davey; Nicholas J Chandler; Assaf Elazar; Jonathan Y Weinstein; Julie V Nguyen; Raphael Trenker; Ryan S Cross; Misty R Jenkins; Melissa J Call; Matthew E Call; Sarel J Fleishman
Publié dans: Crossref, Numéro 1, 2022, ISSN 2050-084X
Éditeur: eLife Sciences Publications
DOI: 10.7554/elife.75660

Biomolecular Recognition of the Glycan Neoantigen CA19-9 by Distinct Antibodies

Auteurs: Aliza Borenstein-Katz, Shira Warszawski, Ron Amon, Maayan Eilon, Hadas Cohen-Dvashi, Shani Leviatan Ben-Arye, Nova Tasnima, Hai Yu, Xi Chen, Vered Padler-Karavani, Sarel Jacob Fleishman, Ron Diskin
Publié dans: Journal of Molecular Biology, Numéro 433/15, 2021, Page(s) 167099, ISSN 0022-2836
Éditeur: Academic Press
DOI: 10.1016/j.jmb.2021.167099

Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning

Auteurs: Alison C. Leonard; Jonathan Jacob Weinstein; Paul J. Steiner; Annette H Erbse; Sarel J. Fleishman; Timothy A. Whitehead
Publié dans: Protein Engineering Design and Selection, Numéro 1, 2022, ISSN 1741-0126
Éditeur: Oxford University Press
DOI: 10.1101/2021.11.22.469552

Combinatorial assembly and design of enzymes

Auteurs: Lipsh-Sokolik, R., Khersonsky O, Schröder, S. P., de Boer, C., Hoch S, Davies, G. J.; Overkleeft, H. S., Fleishman, S. J.
Publié dans: Science magazine, 2023, ISSN 0036-8075
Éditeur: American Association for the Advancement of Science
DOI: 10.1126/science.ade9434

Computationally designed hyperactive Cas9 enzymes

Auteurs: Vos, P. D.; Rossetti, G.; Mantegna, J. L.; Siira, S. J.; Gandadireja, A. P.; Bruce, M.; Raven, S. A.; Khersonsky O; Fleishman, S. J.; Filipovska, A.; Rackham, O
Publié dans: Nature Communications, 2022, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-022-30598-9

A Rationally and Computationally Designed Fluorescent Biosensor for d-Serine

Auteurs: Vanessa Vongsouthi, Jason H. Whitfield, Petr Unichenko, Joshua A. Mitchell, Björn Breithausen, Olga Khersonsky, Leon Kremers, Harald Janovjak, Hiromu Monai, Hajime Hirase, Sarel J. Fleishman, Christian Henneberger, and Colin J. Jackson
Publié dans: ACS Sensors, 2021, ISSN 2379-3694
Éditeur: American Chemical Society
DOI: 10.1021/acssensors.1c01803

Community-Wide Experimental Evaluation of the PROSS Stability-Design Method

Auteurs: Yoav Peleg, Renaud Vincentelli, Brett M. Collins, Kai-En Chen, Emma K. Livingstone, Saroja Weeratunga, Natalya Leneva, Qian Guo, Kim Remans, Kathryn Perez, Gro E.K Bjerga, Øivind Larsen, Ondřej Vaněk, Ondřej Skořepa, Sophie Jacquemin, Arnaud Poterszman, Svend Kjær, Evangelos Christodoulou, Shira Albeck, Orly Dym, Elena Ainbinder, Tamar Unger, Anja Schuetz, Susann Matthes, Michael Bader, Ario
Publié dans: Journal of Molecular Biology, Numéro 433/13, 2021, Page(s) 166964, ISSN 0022-2836
Éditeur: Academic Press
DOI: 10.1016/j.jmb.2021.166964

PROSS 2: a new server for the design of stable and highly expressed protein variants

Auteurs: Jonathan Jacob Weinstein, Adi Goldenzweig, ShlomoYakir Hoch, Sarel Jacob Fleishman
Publié dans: Bioinformatics, Numéro 37/1, 2020, Page(s) 123-125, ISSN 1367-4803
Éditeur: Oxford University Press
DOI: 10.1093/bioinformatics/btaa1071

Designed active-site library reveals thousands of functional GFP variants

Auteurs: Weinstein JY, Martí-Gómez, C.; Lipsh-Sokolik, R.; Hoch SY, Liebermann, D.; Nevo, R.; Weissman, H.; Petrovich-Kopitman, E.; Margulies, D.; Ivankov, D.; McCandlish, D. M.; Fleishman, S. J.
Publié dans: Nature Communications, 2023, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-023-38099-z

Practically useful protein-design methods combining phylogenetic and atomistic calculations

Auteurs: Jonathan Weinstein, Olga Khersonsky, Sarel J Fleishman
Publié dans: Current Opinion in Structural Biology, Numéro 63, 2020, Page(s) 58-64, ISSN 0959-440X
Éditeur: Elsevier BV
DOI: 10.1016/j.sbi.2020.04.003

Design of a basigin‐mimicking inhibitor targeting the malaria invasion protein RH5

Auteurs: Shira Warszawski, Elya Dekel, Ivan Campeotto, Jennifer M. Marshall, Katherine E. Wright, Oliver Lyth, Orli Knop, Neta Regev‐Rudzki, Matthew K. Higgins, Simon J. Draper, Jake Baum, Sarel J. Fleishman
Publié dans: Proteins: Structure, Function, and Bioinformatics, Numéro 88/1, 2019, Page(s) 187-195, ISSN 0887-3585
Éditeur: Wiley-Liss Inc
DOI: 10.1002/prot.25786

Stable mammalian serum albumins designed for bacterial expression

Auteurs: Khersonsky O, Goldsmith M, Zaretsky, I.; Hamer-Rogotner, S.; Dym, O.; Unger T, Yona, M.; Fridmann-Sirkis, Y.; Fleishman, S. J.
Publié dans: Journal of Molecular Biology, 2023, ISSN 0022-2836
Éditeur: Academic Press
DOI: 10.1016/j.jmb.2023.168191

The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes

Auteurs: Rosalie Lipsh‐Sokolik, Dina Listov, Sarel J. Fleishman
Publié dans: Protein Science, Numéro 30/1, 2021, Page(s) 151-159, ISSN 0961-8368
Éditeur: Cold Spring Harbor Laboratory Press
DOI: 10.1002/pro.3970

Extending the New Generation of Structure Predictors to Account for Dynamics and Allostery

Auteurs: Sarel J. Fleishman, Amnon Horovitz
Publié dans: Journal of Molecular Biology, 2021, Page(s) 167007, ISSN 0022-2836
Éditeur: Academic Press
DOI: 10.1016/j.jmb.2021.167007

Computationally designed pyocyanin demethylase acts synergistically with tobramycin to kill recalcitrant Pseudomonas aeruginosa biofilms

Auteurs: Chelsey M. VanDrisse, Rosalie Lipsh-Sokolik, Olga Khersonsky, Sarel J. Fleishman, Dianne K. Newman
Publié dans: Proceedings of the National Academy of Sciences, Numéro 118/12, 2021, Page(s) e2022012118, ISSN 0027-8424
Éditeur: National Academy of Sciences
DOI: 10.1073/pnas.2022012118

Designed high-redox potential laccases exhibit high functional diversity

Auteurs: Shiran Barber-Zucker; Ivan Mateljak; Moshe Goldsmith; Meital Kupervaser; Miguel Alcalde; Sarel J. Fleishman
Publié dans: ACS Catalysis, Numéro 1, 2022, ISSN 2155-5435
Éditeur: American Chemical Society
DOI: 10.1101/2022.06.22.497129

Non-peer reviewed articles (1)

GGAssembler: precise and economical design and synthesis of combinatorial mutation libraries

Auteurs: Shlomo Yakir Hoch, Ravit Netzer, Jonathan Yaacov Weinstein, Lucas Krauss, Karen Hakeny, Sarel Jacob Fleishman
Publié dans: bioRxiv, 2023, ISSN 2692-8205
Éditeur: Cold Spring Harbour
DOI: 10.1101/2023.05.18.541394