Automated computational design of site-targeted repertoires of camelid antibodies

Publicaciones

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

Autores: Olga Khersonsky; Sarel Fleishman
Publicado en: Biodesign Research, Edición 1, 2022, ISSN 0036-8075
Editor: American Association for the Advancement of Science
DOI: 10.34133/2022/9787581

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

Autores: 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
Publicado en: Nature Biotechnology, 2022, ISSN 1087-0156
Editor: Nature Publishing Group
DOI: 10.1038/s41587-021-01162-5

Stable and Functionally Diverse Versatile Peroxidases Designed Directly from Sequences.

Autores: Shiran Barber-Zucker; Vladimir Mindel; Eva Garcia-Ruiz; Jonathan J. Weinstein; Miguel Alcalde; Sarel J. Fleishman
Publicado en: Journal of the American Chemical Society, Edición 1, 2022, ISSN 0002-7863
Editor: American Chemical Society
DOI: 10.1021/jacs.1c12433

Reliable energy-based antibody humanization and stabilization

Autores: 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
Publicado en: Nature Biomedical Engineering, Edición 1, 2023, ISSN 2157-846X
Editor: Springer Nature
DOI: 10.1038/s41551-023-01079-1

Assessing and enhancing foldability in designed proteins

Autores: Dina Listov; Rosalie Lipsh-Sokolik; Stéphane Rosset; Che Yang; Bruno E Correia; Sarel J Fleishman
Publicado en: Protein Science, Edición 1, 2022, ISSN 1469-896X
Editor: Wiley-Blackwell
DOI: 10.1101/2021.11.09.467863

De novo-designed transmembrane domains tune engineered receptor functions

Autores: 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
Publicado en: Crossref, Edición 1, 2022, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.75660

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

Autores: 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
Publicado en: Journal of Molecular Biology, Edición 433/15, 2021, Página(s) 167099, ISSN 0022-2836
Editor: 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

Autores: Alison C. Leonard; Jonathan Jacob Weinstein; Paul J. Steiner; Annette H Erbse; Sarel J. Fleishman; Timothy A. Whitehead
Publicado en: Protein Engineering Design and Selection, Edición 1, 2022, ISSN 1741-0126
Editor: Oxford University Press
DOI: 10.1101/2021.11.22.469552

Combinatorial assembly and design of enzymes

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

Computationally designed hyperactive Cas9 enzymes

Autores: 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
Publicado en: Nature Communications, 2022, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-022-30598-9

A Rationally and Computationally Designed Fluorescent Biosensor for d-Serine

Autores: 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
Publicado en: ACS Sensors, 2021, ISSN 2379-3694
Editor: American Chemical Society
DOI: 10.1021/acssensors.1c01803

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

Autores: 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
Publicado en: Journal of Molecular Biology, Edición 433/13, 2021, Página(s) 166964, ISSN 0022-2836
Editor: Academic Press
DOI: 10.1016/j.jmb.2021.166964

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

Autores: Jonathan Jacob Weinstein, Adi Goldenzweig, ShlomoYakir Hoch, Sarel Jacob Fleishman
Publicado en: Bioinformatics, Edición 37/1, 2020, Página(s) 123-125, ISSN 1367-4803
Editor: Oxford University Press
DOI: 10.1093/bioinformatics/btaa1071

Designed active-site library reveals thousands of functional GFP variants

Autores: 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.
Publicado en: Nature Communications, 2023, ISSN 2041-1723
Editor: Nature Publishing Group
DOI: 10.1038/s41467-023-38099-z

Practically useful protein-design methods combining phylogenetic and atomistic calculations

Autores: Jonathan Weinstein, Olga Khersonsky, Sarel J Fleishman
Publicado en: Current Opinion in Structural Biology, Edición 63, 2020, Página(s) 58-64, ISSN 0959-440X
Editor: Elsevier BV
DOI: 10.1016/j.sbi.2020.04.003

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

Autores: 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
Publicado en: Proteins: Structure, Function, and Bioinformatics, Edición 88/1, 2019, Página(s) 187-195, ISSN 0887-3585
Editor: Wiley-Liss Inc
DOI: 10.1002/prot.25786

Stable mammalian serum albumins designed for bacterial expression

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

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

Autores: Rosalie Lipsh‐Sokolik, Dina Listov, Sarel J. Fleishman
Publicado en: Protein Science, Edición 30/1, 2021, Página(s) 151-159, ISSN 0961-8368
Editor: Cold Spring Harbor Laboratory Press
DOI: 10.1002/pro.3970

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

Autores: Sarel J. Fleishman, Amnon Horovitz
Publicado en: Journal of Molecular Biology, 2021, Página(s) 167007, ISSN 0022-2836
Editor: Academic Press
DOI: 10.1016/j.jmb.2021.167007

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

Autores: Chelsey M. VanDrisse, Rosalie Lipsh-Sokolik, Olga Khersonsky, Sarel J. Fleishman, Dianne K. Newman
Publicado en: Proceedings of the National Academy of Sciences, Edición 118/12, 2021, Página(s) e2022012118, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.2022012118

Designed high-redox potential laccases exhibit high functional diversity

Autores: Shiran Barber-Zucker; Ivan Mateljak; Moshe Goldsmith; Meital Kupervaser; Miguel Alcalde; Sarel J. Fleishman
Publicado en: ACS Catalysis, Edición 1, 2022, ISSN 2155-5435
Editor: American Chemical Society
DOI: 10.1101/2022.06.22.497129

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

Autores: Shlomo Yakir Hoch, Ravit Netzer, Jonathan Yaacov Weinstein, Lucas Krauss, Karen Hakeny, Sarel Jacob Fleishman
Publicado en: bioRxiv, 2023, ISSN 2692-8205
Editor: Cold Spring Harbour
DOI: 10.1101/2023.05.18.541394

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