Andrzej Kolinski Research Group

Coarse-grained protein modeling

Modeling Software & Servers

Biomolecules — dynamics & interactions


KnotProt: a database of proteins with knots and slipknots


Nucleic Acids Research, 43: D306-D314, 2015


The protein topology database KnotProt, , 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.