Zobrazeno 1 - 10
of 10
pro vyhledávání: '"Aleksandra I Jarmolinska"'
Autor:
Vasilina Zayats, Agata P Perlinska, Aleksandra I Jarmolinska, Borys Jastrzebski, Stanislaw Dunin-Horkawicz, Joanna I Sulkowska
Publikováno v:
PLoS Computational Biology, Vol 17, Iss 10, p e1009502 (2021)
While the slipknot topology in proteins has been known for over a decade, its evolutionary origin is still a mystery. We have identified a previously overlooked slipknot motif in a family of two-domain membrane transporters. Moreover, we found that t
Externí odkaz:
https://doaj.org/article/f105ce84f84c4826ad5083eca7f3d2ec
Autor:
Aleksandra I. Jarmolinska, Vasilina Zayats, Agata P. Perlinska, Borys Jastrzebski, Stanislaw Dunin-Horkawicz, Joanna I. Sulkowska
Publikováno v:
PLoS Computational Biology, Vol 17, Iss 10, p e1009502 (2021)
PLoS Computational Biology
PLoS Computational Biology
While the slipknot topology in proteins has been known for over a decade, its evolutionary origin is still a mystery. We have identified a previously overlooked slipknot motif in a family of two-domain membrane transporters. Moreover, we found that t
Autor:
John Lamb, Arne Elofsson, Mirco Michel, Joanna I. Sulkowska, Aleksandra I. Jarmolinska, David Menéndez-Hurtado
Publikováno v:
Journal of Molecular Biology. 431:2442-2448
At present, about half of the protein domain families lack a structural representative. However, in the last decade, predicting contact maps and using these to model the tertiary structure for these protein families have become an alternative approac
Autor:
Helen M. Ginn, Peter Virnau, Benjamin Trefz, Aleksandra I. Jarmolinska, Robert Runkel, Agata P. Perlinska, Joanna I. Sulkowska
Publikováno v:
Journal of Molecular Biology. 431:244-257
Knots in proteins are increasingly being recognized as an important structural concept, and the folding of these peculiar structures still poses considerable challenges. From a functional point of view, most protein knots discovered so far are either
Publikováno v:
Bioinformatics. 36:953-955
Summary The biggest hurdle in studying topology in biopolymers is the steep learning curve for actually seeing the knots in structure visualization. Knot_pull is a command line utility designed to simplify this process—it presents the user with a s
Publikováno v:
Journal of chemical information and modeling. 59(2)
Direct coupling analysis (DCA) is a statistical modeling framework designed to uncover relevant molecular evolutionary relationships from biological sequences. Although DCA has been successfully used in several applications, mapping and visualizing o
Autor:
Peter Virnau, Wanda Niemyska, Szymon Niewieczerzal, Joanna I. Sulkowska, Aleksandra I. Jarmolinska, Jonathan Tammo Siebert
Publikováno v:
Nucleic Acids Research
The KnotGenome server enables the topological analysis of chromosome model data using three-dimensional coordinate files of chromosomes as input. In particular, it detects prime and composite knots in single chromosomes, and links between chromosomes
Publikováno v:
Bioinformatics (Oxford, England). 34(19)
Motivation Over 25% of protein structures possess unresolved fragments. On the other hand, approximately 6% of protein chains have non-trivial topology (and form knots, slipknots, lassos and links). As the topology is fundamental for the proper funct
Autor:
Aleksandra I. Jarmolinska, Kenneth C. Millett, Wanda Niemyska, Eric J. Rawdon, Joanna I. Sulkowska, Pawel Dabrowski-Tumanski
Publikováno v:
Dabrowski-Tumanski, P; Jarmolinska, AI; Niemyska, W; Rawdon, EJ; Millett, KC; & Sulkowska, JI. (2017). LinkProt: a database collecting information about biological links. NUCLEIC ACIDS RESEARCH, 45(D1), D243-D249. doi: 10.1093/nar/gkw976. UC Santa Barbara: Retrieved from: http://www.escholarship.org/uc/item/25q2r8p1
Nucleic acids research, vol 45, iss D1
Nucleic Acids Research
Nucleic acids research, vol 45, iss D1
Nucleic Acids Research
Protein chains are known to fold into topologically complex shapes, such as knots, slipknots or complex lassos. This complex topology of the chain can be considered as an additional feature of a protein, separate from secondary and tertiary structure
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b3f0cda06236a861f9567adb8a9e6102
http://www.escholarship.org/uc/item/25q2r8p1
http://www.escholarship.org/uc/item/25q2r8p1
Publikováno v:
Journal of physics. Condensed matter : an Institute of Physics journal. 27(35)
Knotted protein chains represent a new motif in protein folds. They have been linked to various diseases, and recent extensive analysis of the Protein Data Bank shows that they constitute 1.5% of all deposited protein structures. Despite thorough the