Zobrazeno 1 - 6
of 6
pro vyhledávání: '"Ziv Ben-Aharon"'
Publikováno v:
BMC Bioinformatics, Vol 24, Iss 1, Pp 1-18 (2023)
Abstract Background Determining a protein’s quaternary state, i.e. the number of monomers in a functional unit, is a critical step in protein characterization. Many proteins form multimers for their activity, and over 50% are estimated to naturally
Externí odkaz:
https://doaj.org/article/a66efeb1f8f24b18b311ff73bedf1f54
Autor:
Tomer Tsaban, Julia K. Varga, Orly Avraham, Ziv Ben-Aharon, Alisa Khramushin, Ora Schueler-Furman
Publikováno v:
Nature Communications, Vol 13, Iss 1, Pp 1-12 (2022)
AlphaFold2 has originally been developed to provide highly accurate predictions of protein monomer structures. Here, the authors present a simple adaptation of AlphaFold2 that enables structural modeling of peptide–protein complexes, and explore th
Externí odkaz:
https://doaj.org/article/498a78dc72be44ae80a6bac350a603c6
Autor:
Julia Koehler Leman, Sergey Lyskov, Steven M. Lewis, Jared Adolf-Bryfogle, Rebecca F. Alford, Kyle Barlow, Ziv Ben-Aharon, Daniel Farrell, Jason Fell, William A. Hansen, Ameya Harmalkar, Jeliazko Jeliazkov, Georg Kuenze, Justyna D. Krys, Ajasja Ljubetič, Amanda L. Loshbaugh, Jack Maguire, Rocco Moretti, Vikram Khipple Mulligan, Morgan L. Nance, Phuong T. Nguyen, Shane Ó Conchúir, Shourya S. Roy Burman, Rituparna Samanta, Shannon T. Smith, Frank Teets, Johanna K. S. Tiemann, Andrew Watkins, Hope Woods, Brahm J. Yachnin, Christopher D. Bahl, Chris Bailey-Kellogg, David Baker, Rhiju Das, Frank DiMaio, Sagar D. Khare, Tanja Kortemme, Jason W. Labonte, Kresten Lindorff-Larsen, Jens Meiler, William Schief, Ora Schueler-Furman, Justin B. Siegel, Amelie Stein, Vladimir Yarov-Yarovoy, Brian Kuhlman, Andrew Leaver-Fay, Dominik Gront, Jeffrey J. Gray, Richard Bonneau
Publikováno v:
Nature Communications, Vol 12, Iss 1, Pp 1-15 (2021)
Computational methods are becoming an increasingly important part of biological research. Using the Rosetta framework as an example, the authors demonstrate how community-driven development of computational methods can be done in a reproducible and r
Externí odkaz:
https://doaj.org/article/7ccba8c202cd473d906c246ef7b2eb77
Autor:
Orly Avraham, Tomer Tsaban, Alisa Khramushin, Ora Schueler-Furman, Ziv Ben-Aharon, Julia Varga
Highly accurate protein structure predictions by the recently published deep neural networks such as AlphaFold2 and RoseTTAFold are truly impressive achievements, and will have a tremendous impact far beyond structural biology. If peptide-protein bin
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::75370ea461bf595276baa6f4a8b19c49
https://doi.org/10.1101/2021.08.01.454656
https://doi.org/10.1101/2021.08.01.454656
Autor:
Dominik Gront, Kresten Lindorff-Larsen, Jack Maguire, Jens Meiler, Christopher D. Bahl, Jason S. Fell, Chris Bailey-Kellogg, Andrew M. Watkins, Frank DiMaio, Daniel P. Farrell, Jared Adolf-Bryfogle, Julia Koehler Leman, Frank D. Teets, Vladimir Yarov-Yarovoy, Ajasja Ljubetič, Shannon T. Smith, William A. Hansen, Steven M. Lewis, Justyna Krys, Shourya S. Roy Burman, Amelie Stein, Rhiju Das, David Baker, Vikram Khipple Mulligan, Jason W. Labonte, Georg Kuenze, William R. Schief, Rebecca F. Alford, Shane Ó Conchúir, Hope Woods, Tanja Kortemme, Johanna K. S. Tiemann, Sagar D. Khare, Sergey Lyskov, Ziv Ben-Aharon, Ora Schueler-Furman, Amanda L. Loshbaugh, Richard Bonneau, Brahm J. Yachnin, Andrew Leaver-Fay, Kyle A. Barlow, Phuong T. Nguyen, Jeliazko R. Jeliazkov, Jeffrey J. Gray, Justin B. Siegel, Rocco Moretti, Ameya Harmalkar, Brian Kuhlman
Each year vast international resources are wasted on irreproducible research. The scientific community has been slow to adopt standard software engineering practices, despite the increases in high-dimensional data, complexities of workflows, and comp
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::7ae3b538a88ca76a15e111345bd76765
https://doi.org/10.1101/2021.04.04.438423
https://doi.org/10.1101/2021.04.04.438423
Publikováno v:
Structure. 26:1546-1554.e2
Summary At resolutions worse than 3.5 A, the electron density is weak or nonexistent at the locations of the side chains. Consequently, the assignment of the protein sequences to their correct positions along the backbone is a difficult problem. In t