دورية أكاديمية
AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods.
| العنوان: | AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods. |
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| المؤلفون: | Niemyska W; Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland.; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland., Rubach P; Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland.; Warsaw School of Economics,Al. Niepodleglosci 162, 02-554, Warsaw, Poland., Gren BA; Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland., Nguyen ML; Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland.; Polish-Japanese Academy of Information Technology, Koszykowa 86, 02-008 Warsaw, Poland., Garstka W; Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland.; Inter-faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland., Bruno da Silva F; Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland., Rawdon EJ; University of St. Thomas, 2115 Summit Ave, Saint Paul, MN 55105, USA., Sulkowska JI; Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland. |
| المصدر: | Nucleic acids research [Nucleic Acids Res] 2022 Jul 05; Vol. 50 (W1), pp. W44-W50. |
| نوع المنشور: | Journal Article; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: 1992- : Oxford : Oxford University Press Original Publication: London, Information Retrieval ltd. |
| مواضيع طبية MeSH: | Computers* , Peptides*/chemistry , Protein Conformation*, Models, Molecular ; Proteome ; Databases, Protein |
| مستخلص: | AlphaKnot is a server that measures entanglement in AlphaFold-solved protein models while considering pLDDT confidence values. AlphaKnot has two main functions: (i) providing researchers with a webserver for analyzing knotting in their own AlphaFold predictions and (ii) providing a database of knotting in AlphaFold predictions from the 21 proteomes for which models have been published prior to 2022. The knotting is defined in a probabilistic fashion. The knotting complexity of proteins is presented in the form of a matrix diagram which shows users the knot type for the entire polypeptide chain and for each of its subchains. The dominant knot types as well as the computed locations of the knot cores (i.e. minimal portions of protein backbones that form a given knot type) are shown for each protein structure. Based mainly on the pLDDT confidence values, entanglements are classified as Knots, Unsure, and Artifacts. The database portion of the server can be used, for example, to examine protein geometry and entanglement-function correlations, as a reference set for protein modeling, and for facilitating evolutional studies. The AlphaKnot server can be found at https://alphaknot.cent.uw.edu.pl/. (© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.) |
| المشرفين على المادة: | 0 (Peptides) 0 (Proteome) |
| تواريخ الأحداث: | Date Created: 20220524 Date Completed: 20230410 Latest Revision: 20230412 |
| رمز التحديث: | 20240628 |
| مُعرف محوري في PubMed: | PMC9252816 |
| DOI: | 10.1093/nar/gkac388 |
| PMID: | 35609987 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1362-4962 |
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| DOI: | 10.1093/nar/gkac388 |