Automated computational design of site-targeted repertoires of camelid antibodies

Publikacje

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

Autorzy: Olga Khersonsky; Sarel Fleishman
Opublikowane w: Biodesign Research, Numer 1, 2022, ISSN 0036-8075
Wydawca: American Association for the Advancement of Science
DOI: 10.34133/2022/9787581

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

Autorzy: 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
Opublikowane w: Nature Biotechnology, 2022, ISSN 1087-0156
Wydawca: Nature Publishing Group
DOI: 10.1038/s41587-021-01162-5

Stable and Functionally Diverse Versatile Peroxidases Designed Directly from Sequences.

Autorzy: Shiran Barber-Zucker; Vladimir Mindel; Eva Garcia-Ruiz; Jonathan J. Weinstein; Miguel Alcalde; Sarel J. Fleishman
Opublikowane w: Journal of the American Chemical Society, Numer 1, 2022, ISSN 0002-7863
Wydawca: American Chemical Society
DOI: 10.1021/jacs.1c12433

Reliable energy-based antibody humanization and stabilization

Autorzy: 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
Opublikowane w: Nature Biomedical Engineering, Numer 1, 2023, ISSN 2157-846X
Wydawca: Springer Nature
DOI: 10.1038/s41551-023-01079-1

Assessing and enhancing foldability in designed proteins

Autorzy: Dina Listov; Rosalie Lipsh-Sokolik; Stéphane Rosset; Che Yang; Bruno E Correia; Sarel J Fleishman
Opublikowane w: Protein Science, Numer 1, 2022, ISSN 1469-896X
Wydawca: Wiley-Blackwell
DOI: 10.1101/2021.11.09.467863

De novo-designed transmembrane domains tune engineered receptor functions

Autorzy: 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
Opublikowane w: Crossref, Numer 1, 2022, ISSN 2050-084X
Wydawca: eLife Sciences Publications
DOI: 10.7554/elife.75660

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

Autorzy: 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
Opublikowane w: Journal of Molecular Biology, Numer 433/15, 2021, Strona(/y) 167099, ISSN 0022-2836
Wydawca: 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

Autorzy: Alison C. Leonard; Jonathan Jacob Weinstein; Paul J. Steiner; Annette H Erbse; Sarel J. Fleishman; Timothy A. Whitehead
Opublikowane w: Protein Engineering Design and Selection, Numer 1, 2022, ISSN 1741-0126
Wydawca: Oxford University Press
DOI: 10.1101/2021.11.22.469552

Combinatorial assembly and design of enzymes

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

Computationally designed hyperactive Cas9 enzymes

Autorzy: 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
Opublikowane w: Nature Communications, 2022, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-022-30598-9

A Rationally and Computationally Designed Fluorescent Biosensor for d-Serine

Autorzy: 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
Opublikowane w: ACS Sensors, 2021, ISSN 2379-3694
Wydawca: American Chemical Society
DOI: 10.1021/acssensors.1c01803

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

Autorzy: 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
Opublikowane w: Journal of Molecular Biology, Numer 433/13, 2021, Strona(/y) 166964, ISSN 0022-2836
Wydawca: Academic Press
DOI: 10.1016/j.jmb.2021.166964

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

Autorzy: Jonathan Jacob Weinstein, Adi Goldenzweig, ShlomoYakir Hoch, Sarel Jacob Fleishman
Opublikowane w: Bioinformatics, Numer 37/1, 2020, Strona(/y) 123-125, ISSN 1367-4803
Wydawca: Oxford University Press
DOI: 10.1093/bioinformatics/btaa1071

Designed active-site library reveals thousands of functional GFP variants

Autorzy: 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.
Opublikowane w: Nature Communications, 2023, ISSN 2041-1723
Wydawca: Nature Publishing Group
DOI: 10.1038/s41467-023-38099-z

Practically useful protein-design methods combining phylogenetic and atomistic calculations

Autorzy: Jonathan Weinstein, Olga Khersonsky, Sarel J Fleishman
Opublikowane w: Current Opinion in Structural Biology, Numer 63, 2020, Strona(/y) 58-64, ISSN 0959-440X
Wydawca: Elsevier BV
DOI: 10.1016/j.sbi.2020.04.003

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

Autorzy: 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
Opublikowane w: Proteins: Structure, Function, and Bioinformatics, Numer 88/1, 2019, Strona(/y) 187-195, ISSN 0887-3585
Wydawca: Wiley-Liss Inc
DOI: 10.1002/prot.25786

Stable mammalian serum albumins designed for bacterial expression

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

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

Autorzy: Rosalie Lipsh‐Sokolik, Dina Listov, Sarel J. Fleishman
Opublikowane w: Protein Science, Numer 30/1, 2021, Strona(/y) 151-159, ISSN 0961-8368
Wydawca: Cold Spring Harbor Laboratory Press
DOI: 10.1002/pro.3970

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

Autorzy: Sarel J. Fleishman, Amnon Horovitz
Opublikowane w: Journal of Molecular Biology, 2021, Strona(/y) 167007, ISSN 0022-2836
Wydawca: Academic Press
DOI: 10.1016/j.jmb.2021.167007

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

Autorzy: Chelsey M. VanDrisse, Rosalie Lipsh-Sokolik, Olga Khersonsky, Sarel J. Fleishman, Dianne K. Newman
Opublikowane w: Proceedings of the National Academy of Sciences, Numer 118/12, 2021, Strona(/y) e2022012118, ISSN 0027-8424
Wydawca: National Academy of Sciences
DOI: 10.1073/pnas.2022012118

Designed high-redox potential laccases exhibit high functional diversity

Autorzy: Shiran Barber-Zucker; Ivan Mateljak; Moshe Goldsmith; Meital Kupervaser; Miguel Alcalde; Sarel J. Fleishman
Opublikowane w: ACS Catalysis, Numer 1, 2022, ISSN 2155-5435
Wydawca: American Chemical Society
DOI: 10.1101/2022.06.22.497129

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

Autorzy: Shlomo Yakir Hoch, Ravit Netzer, Jonathan Yaacov Weinstein, Lucas Krauss, Karen Hakeny, Sarel Jacob Fleishman
Opublikowane w: bioRxiv, 2023, ISSN 2692-8205
Wydawca: Cold Spring Harbour
DOI: 10.1101/2023.05.18.541394

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