Title
LinkProt: A database collecting information about biological links
Department/School
Mathematics
Date
10-28-2016
Document Type
Article
Keywords
LinkProt, knot theory, protein chains, complex topologies
Abstract
Protein chains are known to fold into topologically complex shapes, such as knots, slipknots or complex lassos. This complex topology of the chain can be considered as an additional feature of a protein, separate from secondary and tertiary structures. Moreover, the complex topology can be defined also as one additional structural level. The LinkProt database (http://linkprot.cent.uw.edu.pl) collects and displays information about protein links — topologically non-trivial structures made by up to four chains and complexes of chains (e.g. in capsids). The database presents deterministic links (with loops closed, e.g. by two disulfide bonds), links formed probabilistically and macromolecular links. The structures are classified according to their topology and presented using the minimal surface area method. The database is also equipped with basic tools which allow users to analyze the topology of arbitrary (bio)polymers.
Published in
Nucleic Acid Research
Citation/Other Information
Dabrowski-Tumanski, P., Jarmolinska, A. I., Niemyska, W., Rawdon, E. J., Millett, K. C., & Sulkowska, J. I. (2017). LinkProt: a database collecting information about biological links. Nucleic Acids Research, 45(D1), D243–D249. https://doi.org/10.1093/nar/gkw976