Title

KnotProt: a database of proteins with knots and slipknots

Department/School

Mathematics

Date

1-28-2015

Document Type

Article

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.

Volume

43

Issue

1

Published in

Nucleic Acid Research

Citation/Other Information

Jamroz, M., Niemyska, W., Rawdon, E. J., Stasiak, A., Millett, K. C., Sułkowski, P., & Sulkowska, J. I. (2015). KnotProt: A database of proteins with knots and slipknots. Nucleic Acids Research, 43(1), D306–D314. https://doi.org/10.1093/nar/gku1059

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