Send to

Choose Destination
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

Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
Institute of Mathematics, University of Silesia, Bankowa 14, 40-007 Katowice, Poland.
Department of Mathematics, University of St. Thomas, Saint Paul, MN 55105, USA.
Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland
Department of Mathematics, University of California, Santa Barbara, CA 93106, USA.
Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland California Institute of Technology, Pasadena, CA 91125, USA
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


The protein topology database KnotProt,, 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.

[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center