Zobrazeno 1 - 9
of 9
pro vyhledávání: '"Gideon Lapidoth"'
Autor:
Gideon Lapidoth, Olga Khersonsky, Rosalie Lipsh, Orly Dym, Shira Albeck, Shelly Rogotner, Sarel J. Fleishman
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-9 (2018)
Computationally designed enzymes often show lower activity or stability than their natural counterparts. Here, the authors present an evolution-inspired method for automated enzyme design, creating stable enzymes with accurate active site architectur
Externí odkaz:
https://doaj.org/article/e6f62792433646fab21959e1b02b0675
Autor:
Sarel J. Fleishman, Tamar Unger, Orly Dym, Gideon Lapidoth, Dror Baran, Christoffer Norn, M. Gabriele Pszolla, Michael D. Tyka, Shira Albeck
Publikováno v:
'Proceedings of the National Academy of Sciences of the USA ', vol: 114, pages: 10900-10905 (2017)
Natural proteins must both fold into a stable conformation and exert their molecular function. To date, computational design has successfully produced stable and atomically accurate proteins by using so-called “ideal” folds rich in regular second
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ef1c342215d7886ea7d0abf6c21ed120
https://epn-library.esrf.fr/flora/jsp/index_view_direct_anonymous.jsp?record=doc:PUB_ESRF:48191
https://epn-library.esrf.fr/flora/jsp/index_view_direct_anonymous.jsp?record=doc:PUB_ESRF:48191
Publikováno v:
Bioinformatics. 35:1591-1593
Summary Methods for antibody structure prediction rely on sequence homology to experimentally determined structures. Resulting models may be accurate but are often stereochemically strained, limiting their usefulness in modeling and design workflows.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::99bd5c2b334b6a4c1563bff8b8260e6b
https://doi.org/10.1093/bioinformatics/bty822
https://doi.org/10.1093/bioinformatics/bty822
Autor:
Jack Maguire, Ragul Gowthaman, Marion F. Sauer, Georg Kuenze, Tanja Kortemme, Benjamin Basanta, Indigo Chris King, Jens Meiler, Rhiju Das, Ora Schueler-Furman, Nicholas A. Marze, Brandon Frenz, Christoffer Norn, Julia Koehler Leman, Jason W. Labonte, Kala Bharath Pilla, Lei Shi, Sergey Lyskov, Brian D. Weitzner, Nir London, Karen R. Khar, Jaume Bonet, Nawsad Alam, Andreas Scheck, Alexander M. Sevy, Lars Malmström, Thomas Huber, Christopher Bystroff, Lior Zimmerman, Lorna Dsilva, Bruno E. Correia, Roland L. Dunbrack, Sergey Ovchinnikov, Rocco Moretti, Scott Horowitz, Phil Bradley, Frank DiMaio, Noah Ollikainen, Brian Kuhlman, Jeffrey J. Gray, Melanie L. Aprahamian, Andrew Leaver-Fay, Santrupti Nerli, Brian Koepnick, Xingjie Pan, Manasi A. Pethe, Andrew M. Watkins, Summer B. Thyme, Enrique Marcos, Vikram Khipple Mulligan, Hahnbeom Park, Po-Ssu Huang, David K. Johnson, Daniel-Adriano Silva, Patrick Barth, Shannon Smith, Caleb Geniesse, Jason K. Lai, Patrick Conway, Amelie Stein, Jeliazko R. Jeliazkov, David Baker, Dominik Gront, Kalli Kappel, Firas Khatib, Robert Kleffner, Brian J. Bender, Richard Bonneau, Kyle A. Barlow, Joseph H. Lubin, Shourya S. Roy Burman, Nikolaos G. Sgourakis, Yuval Sedan, Ryan E. Pavlovicz, Kristin Blacklock, Seth Cooper, Barak Raveh, Alisa Khramushin, John Karanicolas, Justin B. Siegel, Sharon L. Guffy, Brian G. Pierce, Alex Ford, Darwin Y. Fu, Orly Marcu, Gideon Lapidoth, Brian Coventry, René M. de Jong, Shane O’Conchúir, Thomas W. Linsky, William R. Schief, Rebecca F. Alford, Scott E. Boyken, Sagar D. Khare, Maria Szegedy, Ray Yu-Ruei Wang, Steven M. Lewis, Hamed Khakzad, Timothy M. Jacobs, Frank D. Teets, Lukasz Goldschmidt, Daisuke Kuroda, Steffen Lindert, P. Douglas Renfrew, Yifan Song, Jared Adolf-Bryfogle, Michael S. Pacella, Aliza B. Rubenstein
Publikováno v:
Nat Methods
The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactore
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c561276e840d68005d2aab06fb9642da
https://pubmed.ncbi.nlm.nih.gov/32483333
https://pubmed.ncbi.nlm.nih.gov/32483333
Publikováno v:
Proteins: Structure, Function, and Bioinformatics. 85:30-38
Current methods for antibody structure prediction rely on sequence homology to known structures. Although this strategy often yields accurate predictions, models can be stereo-chemically strained. Here, we present a fully automated algorithm, called
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::0c36a3dd9ac12d438d8217469d62241d
https://doi.org/10.1002/prot.25185
https://doi.org/10.1002/prot.25185
Autor:
Shelly Rogotner, Olga Khersonsky, Sarel J. Fleishman, Shira Albeck, Rosalie Lipsh, Gideon Lapidoth, Orly Dym
Publikováno v:
Nature Communications
Nature Communications, Vol 9, Iss 1, Pp 1-9 (2018)
Nature Communications, Vol 9, Iss 1, Pp 1-9 (2018)
Automated design of enzymes with wild-type-like catalytic properties has been a long-standing but elusive goal. Here, we present a general, automated method for enzyme design through combinatorial backbone assembly. Starting from a set of homologous
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::51c11ef226751f33d1fddc2011ffeeb8
https://doi.org/10.1038/s41467-018-05205-5
https://doi.org/10.1038/s41467-018-05205-5
Autor:
Dror Baran, Sarel J. Fleishman, Michael D. Tyka, Christoffer Norn, Assaf Alon, Gabriele M. Pszolla, Gideon Lapidoth
Publikováno v:
Proteins: Structure, Function, and Bioinformatics. 83:1385-1406
Computational design of protein function has made substantial progress, generating new enzymes, binders, inhibitors, and nanomaterials not previously seen in nature. However, the ability to design new protein backbones for function--essential to exer
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::67154d4d094f4e366b870c615febcd28
https://doi.org/10.1002/prot.24779
https://doi.org/10.1002/prot.24779
Autor:
Ohad Mazor, Ronit Rosenfeld, Eyal Epstein, Sarel J. Fleishman, Adva Mechaly, Chanoch Kronman, Ron Alcalay, Gideon Lapidoth
Publikováno v:
Protein engineering, designselection : PEDS. 30(9)
While potent monoclonal antibodies against ricin were introduced over the years, the question whether increasing antibody affinity enables better toxin neutralization was not fully addressed yet. The aim of this study was to characterize the contribu
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4736c1493cad83eba9ede3a1585c8a0b
https://pubmed.ncbi.nlm.nih.gov/28472478
https://pubmed.ncbi.nlm.nih.gov/28472478
Publikováno v:
Proteins. 85(1)
Current methods for antibody structure prediction rely on sequence homology to known structures. Although this strategy often yields accurate predictions, models can be stereo-chemically strained. Here, we present a fully automated algorithm, called
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::94a1ff7884d1044b1bcb8fdc482cfae1
https://pubmed.ncbi.nlm.nih.gov/27717001
https://pubmed.ncbi.nlm.nih.gov/27717001