Zobrazeno 1 - 10
of 80
pro vyhledávání: '"Amelie, Stein"'
SSEmb: A joint embedding of protein sequence and structure enables robust variant effect predictions
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-9 (2024)
Abstract The ability to predict how amino acid changes affect proteins has a wide range of applications including in disease variant classification and protein engineering. Many existing methods focus on learning from patterns found in either protein
Externí odkaz:
https://doaj.org/article/535ce70394734b42995cf8a092ec6220
Autor:
Martin Grønbæk-Thygesen, Vasileios Voutsinos, Kristoffer E. Johansson, Thea K. Schulze, Matteo Cagiada, Line Pedersen, Lene Clausen, Snehal Nariya, Rachel L. Powell, Amelie Stein, Douglas M. Fowler, Kresten Lindorff-Larsen, Rasmus Hartmann-Petersen
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-18 (2024)
Abstract Unstable proteins are prone to form non-native interactions with other proteins and thereby may become toxic. To mitigate this, destabilized proteins are targeted by the protein quality control network. Here we present systematic studies of
Externí odkaz:
https://doaj.org/article/78779a3126b8415c806c43decd7c4a0b
Autor:
Sarah Gersing, Thea K. Schulze, Matteo Cagiada, Amelie Stein, Frederick P. Roth, Kresten Lindorff-Larsen, Rasmus Hartmann-Petersen
Publikováno v:
Genome Biology, Vol 25, Iss 1, Pp 1-22 (2024)
Abstract Background Amino acid substitutions can perturb protein activity in multiple ways. Understanding their mechanistic basis may pinpoint how residues contribute to protein function. Here, we characterize the mechanisms underlying variant effect
Externí odkaz:
https://doaj.org/article/ae336200514940dba9340a11b8a1aaa3
Autor:
Lene Clausen, Vasileios Voutsinos, Matteo Cagiada, Kristoffer E. Johansson, Martin Grønbæk-Thygesen, Snehal Nariya, Rachel L. Powell, Magnus K. N. Have, Vibe H. Oestergaard, Amelie Stein, Douglas M. Fowler, Kresten Lindorff-Larsen, Rasmus Hartmann-Petersen
Publikováno v:
Nature Communications, Vol 15, Iss 1, Pp 1-17 (2024)
Abstract Proteostasis can be disturbed by mutations affecting folding and stability of the encoded protein. An example is the ubiquitin ligase Parkin, where gene variants result in autosomal recessive Parkinsonism. To uncover the pathological mechani
Externí odkaz:
https://doaj.org/article/6ff4219e4bce40eb81ed52752e8585a9
Autor:
Matteo Cagiada, Sandro Bottaro, Søren Lindemose, Signe M. Schenstrøm, Amelie Stein, Rasmus Hartmann-Petersen, Kresten Lindorff-Larsen
Publikováno v:
Nature Communications, Vol 14, Iss 1, Pp 1-13 (2023)
Abstract Proteins play important roles in biology, biotechnology and pharmacology, and missense variants are a common cause of disease. Discovering functionally important sites in proteins is a central but difficult problem because of the lack of lar
Externí odkaz:
https://doaj.org/article/af06fd69055d4def9da435b0033ad21e
Autor:
Sarah Gersing, Matteo Cagiada, Marinella Gebbia, Anette P. Gjesing, Atina G. Coté, Gireesh Seesankar, Roujia Li, Daniel Tabet, Jochen Weile, Amelie Stein, Anna L. Gloyn, Torben Hansen, Frederick P. Roth, Kresten Lindorff-Larsen, Rasmus Hartmann-Petersen
Publikováno v:
Genome Biology, Vol 24, Iss 1, Pp 1-23 (2023)
Abstract Background Glucokinase (GCK) regulates insulin secretion to maintain appropriate blood glucose levels. Sequence variants can alter GCK activity to cause hyperinsulinemic hypoglycemia or hyperglycemia associated with GCK-maturity-onset diabet
Externí odkaz:
https://doaj.org/article/f21cc0a236d84a9c9c7553a60799c36e
Autor:
Audrone Valanciute, Lasse Nygaard, Henrike Zschach, Michael Maglegaard Jepsen, Kresten Lindorff-Larsen, Amelie Stein
Publikováno v:
Computational and Structural Biotechnology Journal, Vol 21, Iss , Pp 66-73 (2023)
Calculating changes in protein stability (ΔΔG) has been shown to be central for predicting the consequences of single amino acid substitutions in protein engineering as well as interpretation of genomic variants for disease risk. Structure-based ca
Externí odkaz:
https://doaj.org/article/604ea8862e664c0f92339efdbbb4177c
Autor:
Lasse M Blaabjerg, Maher M Kassem, Lydia L Good, Nicolas Jonsson, Matteo Cagiada, Kristoffer E Johansson, Wouter Boomsma, Amelie Stein, Kresten Lindorff-Larsen
Publikováno v:
eLife, Vol 12 (2023)
Predicting the thermodynamic stability of proteins is a common and widely used step in protein engineering, and when elucidating the molecular mechanisms behind evolution and disease. Here, we present RaSP, a method for making rapid and accurate pred
Externí odkaz:
https://doaj.org/article/01b275426b464bf48875b519f6242bee
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:
Fia B. Larsen, Matteo Cagiada, Jonas Dideriksen, Amelie Stein, Kresten Lindorff-Larsen, Rasmus Hartmann-Petersen
Publikováno v:
Biochemistry. 62:1394-1405
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::2bcf20a1c1359d6ff31487f788088883
https://doi.org/10.1021/acs.biochem.3c00008
https://doi.org/10.1021/acs.biochem.3c00008