Zobrazeno 1 - 10
of 52
pro vyhledávání: '"Rachel Kolodny"'
Publikováno v:
PLoS Computational Biology, Vol 18, Iss 2, p e1009833 (2022)
As sequence and structure comparison algorithms gain sensitivity, the intrinsic interconnectedness of the protein universe has become increasingly apparent. Despite this general trend, β-trefoils have emerged as an uncommon counterexample: They are
Externí odkaz:
https://doaj.org/article/9bccdd6f8ba340e490e0f0b1d59d2993
Autor:
Liam M Longo, Jagoda Jabłońska, Pratik Vyas, Manil Kanade, Rachel Kolodny, Nir Ben-Tal, Dan S Tawfik
Publikováno v:
eLife, Vol 9 (2020)
This article is dedicated to the memory of Michael G. Rossmann. Dating back to the last universal common ancestor, P-loop NTPases and Rossmanns comprise the most ubiquitous and diverse enzyme lineages. Despite similarities in their overall architectu
Externí odkaz:
https://doaj.org/article/78e631a8267442aaa3cc5e6804dd8ea3
Autor:
Meghan Whitney Franklin, Sergey Nepomnyachyi, Ryan Feehan, Nir Ben-Tal, Rachel Kolodny, Joanna SG Slusky
Publikováno v:
eLife, Vol 7 (2018)
Outer membrane proteins (OMPs) are the proteins in the surface of Gram-negative bacteria. These proteins have diverse functions but a single topology: the β-barrel. Sequence analysis has suggested that this common fold is a β-hairpin repeat protein
Externí odkaz:
https://doaj.org/article/69259f8ebb4d4194a9db6262707ed056
Autor:
Margarita Osadchy, Rachel Kolodny
Publikováno v:
The Journal of Physical Chemistry B. 125:6440-6450
The deep learning revolution introduced a new and efficacious way to address computational challenges in a wide range of fields, relying on large data sets and powerful computational resources. In protein engineering, we consider the challenge of com
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ecdca95fa841b8d469a468bbe11c8a09
https://doi.org/10.1021/acs.jpcb.1c02449
https://doi.org/10.1021/acs.jpcb.1c02449
Publikováno v:
Protein Science. 31
The emergence of novel proteins, beyond these that can be readily made by duplication and recombination of preexisting domains, is elusive. De novo emergence from random sequences is unlikely because the vast majority of random chains would not even
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::dbccdaff6e5106ec492ecf837215f82b
https://doi.org/10.1002/pro.4407
https://doi.org/10.1002/pro.4407
Autor:
Nir Ben-Tal, Rachel Kolodny
Publikováno v:
Structure (London, England : 1993). 30(8)
Accurate protein structure predictors use clusters of homologues, which disregard sequence specific effects. In this issue of Structure, Weißenow and colleagues report a deep learning-based tool, EMBER2, that efficiently predicts the distances in a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f770090716f0779cde0d8bd5745d4722
https://pubmed.ncbi.nlm.nih.gov/35609601
https://pubmed.ncbi.nlm.nih.gov/35609601
Currently known G protein-coupled receptors (GPCRs) have a single transmembrane domain. Many GPCRs form dimers that have two transmembrane domains (one per protein), and there are indications that this dimeric interaction is functionally meaningful.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::e8dba6cd88972fef7b23e6548761faf9
https://doi.org/10.1101/2022.07.26.501653
https://doi.org/10.1101/2022.07.26.501653
Autor:
Ram Doolman, Asaf Vivante, Motti Gerlic, Nir Ben-Tal, Yaniv Lustig, Liran I. Shlush, Shlomit Keler, Keren Asraf, Rachel Kolodny, Danit Atias-Varon, Ekaterina Shlush, Ariel Munitz
Publikováno v:
Clinical Infectious Diseases
Background Coronavirus disease 2019 (COVID-19) and dengue fever are difficult to distinguish given shared clinical and laboratory features. Failing to consider COVID-19 due to false-positive dengue serology can have serious implications. We aimed to
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bff85a5106c322fd1ad54c4d70ed699c
https://doi.org/10.1093/cid/ciaa1207
https://doi.org/10.1093/cid/ciaa1207
Publikováno v:
Proceedings of the National Academy of Sciences of the United States of America
Significance How proteins evolved to recognize and bind their ligands is a key mystery in protein function evolution. To explore this mystery, we study how proteins bind adenine, an ancient fragment. We characterize physicochemical patterns of protei
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a13765f2c847f6bf9086ee2e66d0efa5
https://doi.org/10.1073/pnas.1911349117
https://doi.org/10.1073/pnas.1911349117
Publikováno v:
Proceedings of the National Academy of Sciences of the United States of America
Significance All currently known architectures of outer-membrane beta barrels (OMBBs) have only one barrel. While the vast majority function as oligomers, with barrels from different chains packing against each other in the membrane, it was assumed t
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::199edb8c6a4e40e59fe70e0f49322d24
https://pubmed.ncbi.nlm.nih.gov/34330833
https://pubmed.ncbi.nlm.nih.gov/34330833