Automated computational design of site-targeted repertoires of camelid antibodies

Informazioni relative al progetto

AutoCAb

ID dell’accordo di sovvenzione: 815379

DOI 10.3030/815379

Progetto chiuso

Data della firma CE 10 Dicembre 2018

Data di avvio 1 Gennaio 2019

Data di completamento 31 Dicembre 2023

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale € 2 337 500,00

Contributo UE € 2 337 500,00

Coordinato da

WEIZMANN INSTITUTE OF SCIENCE
Israel

Pubblicazioni

Peer reviewed articles (21)

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

Autori: Olga Khersonsky; Sarel Fleishman
Pubblicato in: Biodesign Research, Numero 1, 2022, ISSN 0036-8075
Editore: American Association for the Advancement of Science
DOI: 10.34133/2022/9787581

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

Autori: 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
Pubblicato in: Nature Biotechnology, 2022, ISSN 1087-0156
Editore: Nature Publishing Group
DOI: 10.1038/s41587-021-01162-5

Stable and Functionally Diverse Versatile Peroxidases Designed Directly from Sequences.

Autori: Shiran Barber-Zucker; Vladimir Mindel; Eva Garcia-Ruiz; Jonathan J. Weinstein; Miguel Alcalde; Sarel J. Fleishman
Pubblicato in: Journal of the American Chemical Society, Numero 1, 2022, ISSN 0002-7863
Editore: American Chemical Society
DOI: 10.1021/jacs.1c12433

Reliable energy-based antibody humanization and stabilization

Autori: 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
Pubblicato in: Nature Biomedical Engineering, Numero 1, 2023, ISSN 2157-846X
Editore: Springer Nature
DOI: 10.1038/s41551-023-01079-1

Assessing and enhancing foldability in designed proteins

Autori: Dina Listov; Rosalie Lipsh-Sokolik; Stéphane Rosset; Che Yang; Bruno E Correia; Sarel J Fleishman
Pubblicato in: Protein Science, Numero 1, 2022, ISSN 1469-896X
Editore: Wiley-Blackwell
DOI: 10.1101/2021.11.09.467863

De novo-designed transmembrane domains tune engineered receptor functions

Autori: 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
Pubblicato in: Crossref, Numero 1, 2022, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.75660

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

Autori: 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
Pubblicato in: Journal of Molecular Biology, Numero 433/15, 2021, Pagina/e 167099, ISSN 0022-2836
Editore: 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

Autori: Alison C. Leonard; Jonathan Jacob Weinstein; Paul J. Steiner; Annette H Erbse; Sarel J. Fleishman; Timothy A. Whitehead
Pubblicato in: Protein Engineering Design and Selection, Numero 1, 2022, ISSN 1741-0126
Editore: Oxford University Press
DOI: 10.1101/2021.11.22.469552

Combinatorial assembly and design of enzymes

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

Computationally designed hyperactive Cas9 enzymes

Autori: 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
Pubblicato in: Nature Communications, 2022, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-022-30598-9

A Rationally and Computationally Designed Fluorescent Biosensor for d-Serine

Autori: 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
Pubblicato in: ACS Sensors, 2021, ISSN 2379-3694
Editore: American Chemical Society
DOI: 10.1021/acssensors.1c01803

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

Autori: 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
Pubblicato in: Journal of Molecular Biology, Numero 433/13, 2021, Pagina/e 166964, ISSN 0022-2836
Editore: Academic Press
DOI: 10.1016/j.jmb.2021.166964

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

Autori: Jonathan Jacob Weinstein, Adi Goldenzweig, ShlomoYakir Hoch, Sarel Jacob Fleishman
Pubblicato in: Bioinformatics, Numero 37/1, 2020, Pagina/e 123-125, ISSN 1367-4803
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btaa1071

Designed active-site library reveals thousands of functional GFP variants

Autori: 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.
Pubblicato in: Nature Communications, 2023, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-023-38099-z

Practically useful protein-design methods combining phylogenetic and atomistic calculations

Autori: Jonathan Weinstein, Olga Khersonsky, Sarel J Fleishman
Pubblicato in: Current Opinion in Structural Biology, Numero 63, 2020, Pagina/e 58-64, ISSN 0959-440X
Editore: Elsevier BV
DOI: 10.1016/j.sbi.2020.04.003

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

Autori: 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
Pubblicato in: Proteins: Structure, Function, and Bioinformatics, Numero 88/1, 2019, Pagina/e 187-195, ISSN 0887-3585
Editore: Wiley-Liss Inc
DOI: 10.1002/prot.25786

Stable mammalian serum albumins designed for bacterial expression

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

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

Autori: Rosalie Lipsh‐Sokolik, Dina Listov, Sarel J. Fleishman
Pubblicato in: Protein Science, Numero 30/1, 2021, Pagina/e 151-159, ISSN 0961-8368
Editore: Cold Spring Harbor Laboratory Press
DOI: 10.1002/pro.3970

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

Autori: Sarel J. Fleishman, Amnon Horovitz
Pubblicato in: Journal of Molecular Biology, 2021, Pagina/e 167007, ISSN 0022-2836
Editore: Academic Press
DOI: 10.1016/j.jmb.2021.167007

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

Autori: Chelsey M. VanDrisse, Rosalie Lipsh-Sokolik, Olga Khersonsky, Sarel J. Fleishman, Dianne K. Newman
Pubblicato in: Proceedings of the National Academy of Sciences, Numero 118/12, 2021, Pagina/e e2022012118, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2022012118

Designed high-redox potential laccases exhibit high functional diversity

Autori: Shiran Barber-Zucker; Ivan Mateljak; Moshe Goldsmith; Meital Kupervaser; Miguel Alcalde; Sarel J. Fleishman
Pubblicato in: ACS Catalysis, Numero 1, 2022, ISSN 2155-5435
Editore: 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

Autori: Shlomo Yakir Hoch, Ravit Netzer, Jonathan Yaacov Weinstein, Lucas Krauss, Karen Hakeny, Sarel Jacob Fleishman
Pubblicato in: bioRxiv, 2023, ISSN 2692-8205
Editore: Cold Spring Harbour
DOI: 10.1101/2023.05.18.541394