title: KnotProt: a database of proteins with knots and slipknots.
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.
authors.affiliation: Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
authors.forename: Michal
authors.initials: M
authors.lastname: Jamroz
authors.affiliation: Institute of Mathematics, University of Silesia, Bankowa 14, 40-007 Katowice, Poland.
authors.forename: Wanda
authors.initials: W
authors.lastname: Niemyska
authors.affiliation: Department of Mathematics, University of St. Thomas, Saint Paul, MN 55105, USA.
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Rawdon
authors.affiliation: Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland jsulkowska@chem.uw.edu.pl.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Stasiak
authors.affiliation: Department of Mathematics, University of California, Santa Barbara, CA 93106, USA.
authors.forename: Kenneth C
authors.initials: KC
authors.lastname: Millett
authors.affiliation: 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.
authors.forename: Piotr
authors.initials: P
authors.lastname: Sułkowski
authors.affiliation: 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.
authors.forename: Joanna I
authors.initials: JI
authors.lastname: Sulkowska
mesh_terms: D030562:Databases, Protein; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation
chemical_list: D010455:Peptides