Automated computational design of site-targeted repertoires of camelid antibodies

Project Information

AutoCAb

Grant agreement ID: 815379

DOI 10.3030/815379

Project closed

EC signature date 10 December 2018

Start date 1 January 2019

End date 31 December 2023

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 2 337 500,00

EU contribution € 2 337 500,00

Coordinated by

WEIZMANN INSTITUTE OF SCIENCE
Israel

Publications

Peer reviewed articles (21)

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

Author(s): Olga Khersonsky; Sarel Fleishman
Published in: Biodesign Research, Issue 1, 2022, ISSN 0036-8075
Publisher: American Association for the Advancement of Science
DOI: 10.34133/2022/9787581

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

Author(s): 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
Published in: Nature Biotechnology, 2022, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-021-01162-5

Stable and Functionally Diverse Versatile Peroxidases Designed Directly from Sequences.

Author(s): Shiran Barber-Zucker; Vladimir Mindel; Eva Garcia-Ruiz; Jonathan J. Weinstein; Miguel Alcalde; Sarel J. Fleishman
Published in: Journal of the American Chemical Society, Issue 1, 2022, ISSN 0002-7863
Publisher: American Chemical Society
DOI: 10.1021/jacs.1c12433

Reliable energy-based antibody humanization and stabilization

Author(s): 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
Published in: Nature Biomedical Engineering, Issue 1, 2023, ISSN 2157-846X
Publisher: Springer Nature
DOI: 10.1038/s41551-023-01079-1

Assessing and enhancing foldability in designed proteins

Author(s): Dina Listov; Rosalie Lipsh-Sokolik; Stéphane Rosset; Che Yang; Bruno E Correia; Sarel J Fleishman
Published in: Protein Science, Issue 1, 2022, ISSN 1469-896X
Publisher: Wiley-Blackwell
DOI: 10.1101/2021.11.09.467863

De novo-designed transmembrane domains tune engineered receptor functions

Author(s): 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
Published in: Crossref, Issue 1, 2022, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.75660

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

Author(s): 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
Published in: Journal of Molecular Biology, Issue 433/15, 2021, Page(s) 167099, ISSN 0022-2836
Publisher: 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

Author(s): Alison C. Leonard; Jonathan Jacob Weinstein; Paul J. Steiner; Annette H Erbse; Sarel J. Fleishman; Timothy A. Whitehead
Published in: Protein Engineering Design and Selection, Issue 1, 2022, ISSN 1741-0126
Publisher: Oxford University Press
DOI: 10.1101/2021.11.22.469552

Combinatorial assembly and design of enzymes

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

Computationally designed hyperactive Cas9 enzymes

Author(s): 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
Published in: Nature Communications, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-30598-9

A Rationally and Computationally Designed Fluorescent Biosensor for d-Serine

Author(s): 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
Published in: ACS Sensors, 2021, ISSN 2379-3694
Publisher: American Chemical Society
DOI: 10.1021/acssensors.1c01803

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

Author(s): 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
Published in: Journal of Molecular Biology, Issue 433/13, 2021, Page(s) 166964, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2021.166964

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

Author(s): Jonathan Jacob Weinstein, Adi Goldenzweig, ShlomoYakir Hoch, Sarel Jacob Fleishman
Published in: Bioinformatics, Issue 37/1, 2020, Page(s) 123-125, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa1071

Designed active-site library reveals thousands of functional GFP variants

Author(s): 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.
Published in: Nature Communications, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-023-38099-z

Practically useful protein-design methods combining phylogenetic and atomistic calculations

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

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

Author(s): 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
Published in: Proteins: Structure, Function, and Bioinformatics, Issue 88/1, 2019, Page(s) 187-195, ISSN 0887-3585
Publisher: Wiley-Liss Inc
DOI: 10.1002/prot.25786

Stable mammalian serum albumins designed for bacterial expression

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

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

Author(s): Rosalie Lipsh‐Sokolik, Dina Listov, Sarel J. Fleishman
Published in: Protein Science, Issue 30/1, 2021, Page(s) 151-159, ISSN 0961-8368
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1002/pro.3970

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

Author(s): Sarel J. Fleishman, Amnon Horovitz
Published in: Journal of Molecular Biology, 2021, Page(s) 167007, ISSN 0022-2836
Publisher: Academic Press
DOI: 10.1016/j.jmb.2021.167007

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

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

Designed high-redox potential laccases exhibit high functional diversity

Author(s): Shiran Barber-Zucker; Ivan Mateljak; Moshe Goldsmith; Meital Kupervaser; Miguel Alcalde; Sarel J. Fleishman
Published in: ACS Catalysis, Issue 1, 2022, ISSN 2155-5435
Publisher: 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

Author(s): Shlomo Yakir Hoch, Ravit Netzer, Jonathan Yaacov Weinstein, Lucas Krauss, Karen Hakeny, Sarel Jacob Fleishman
Published in: bioRxiv, 2023, ISSN 2692-8205
Publisher: Cold Spring Harbour
DOI: 10.1101/2023.05.18.541394