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Nucleic Acids Res. 2015 Jan;43(Database issue):D306-14. doi: 10.1093/nar/gku1059. Epub 2014 Oct 31.

KnotProt: a database of proteins with knots and slipknots.

Author information

1
Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
2
Institute of Mathematics, University of Silesia, Bankowa 14, 40-007 Katowice, Poland.
3
Department of Mathematics, University of St. Thomas, Saint Paul, MN 55105, USA.
4
Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland jsulkowska@chem.uw.edu.pl.
5
Department of Mathematics, University of California, Santa Barbara, CA 93106, USA.
6
Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland California Institute of Technology, Pasadena, CA 91125, USA jsulkowska@chem.uw.edu.pl.
7
Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland jsulkowska@chem.uw.edu.pl.

Abstract

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.

PMID:
25361973
PMCID:
PMC4383900
DOI:
10.1093/nar/gku1059
[Indexed for MEDLINE]
Free PMC Article

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