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KnotProt: a database of proteins with knots and slipknots
The protein topology database KnotProt, http://knotprot.cent.uw.edu.pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots. The knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot typ...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383900/ https://www.ncbi.nlm.nih.gov/pubmed/25361973 http://dx.doi.org/10.1093/nar/gku1059 |
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author | Jamroz, Michal Niemyska, Wanda Rawdon, Eric J. Stasiak, Andrzej Millett, Kenneth C. Sułkowski, Piotr Sulkowska, Joanna I. |
author_facet | Jamroz, Michal Niemyska, Wanda Rawdon, Eric J. Stasiak, Andrzej Millett, Kenneth C. Sułkowski, Piotr Sulkowska, Joanna I. |
author_sort | Jamroz, Michal |
collection | PubMed |
description | The protein topology database KnotProt, http://knotprot.cent.uw.edu.pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots. The knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot. In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting. As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprints. |
format | Online Article Text |
id | pubmed-4383900 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-43839002015-04-08 KnotProt: a database of proteins with knots and slipknots Jamroz, Michal Niemyska, Wanda Rawdon, Eric J. Stasiak, Andrzej Millett, Kenneth C. Sułkowski, Piotr Sulkowska, Joanna I. Nucleic Acids Res Database Issue The protein topology database KnotProt, http://knotprot.cent.uw.edu.pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots. The knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot. In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting. As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprints. Oxford University Press 2014-10-31 2015-01-28 /pmc/articles/PMC4383900/ /pubmed/25361973 http://dx.doi.org/10.1093/nar/gku1059 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Database Issue Jamroz, Michal Niemyska, Wanda Rawdon, Eric J. Stasiak, Andrzej Millett, Kenneth C. Sułkowski, Piotr Sulkowska, Joanna I. KnotProt: a database of proteins with knots and slipknots |
title | KnotProt: a database of proteins with knots and slipknots |
title_full | KnotProt: a database of proteins with knots and slipknots |
title_fullStr | KnotProt: a database of proteins with knots and slipknots |
title_full_unstemmed | KnotProt: a database of proteins with knots and slipknots |
title_short | KnotProt: a database of proteins with knots and slipknots |
title_sort | knotprot: a database of proteins with knots and slipknots |
topic | Database Issue |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383900/ https://www.ncbi.nlm.nih.gov/pubmed/25361973 http://dx.doi.org/10.1093/nar/gku1059 |
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