TY - JOUR T1 - KnotProt: a database of proteins with knots and slipknots JF - Nucleic Acids Research Y1 - 2015 A1 - Michal Jamroz A1 - Wanda Niemyska A1 - Eric J Rawdon A1 - Andrzej Stasiak A1 - Kenneth C Millett A1 - Piotr Sułkowski A1 - Joanna I. Sulkowska AB - 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 catalogued 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 (knots’ core size) or the depth of a knot, i.e. how many aminoacids can be removed from either end of the catalogued protein structure before converting it from a knot to a different type of knot. In addition, the database presents extensive information about the biological function of proteins with non-trivial knotting and the families and fold types of these proteins. As an additional feature, the KnotProt database enables users to submit protein or polymer structures and generate their knotting fingerprints. http://knotprot.cent.uw.edu.pl/ VL - 43 UR - http://nar.oxfordjournals.org/content/43/D1/D306 IS - D1 ER -