title: LinkProt: a database collecting information about biological links.
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.
authors: 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.
authors: Pawel
authors: 0000-0001-9412-1716
authors: P
authors: Dabrowski-Tumanski
authors: Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.|College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
authors: Aleksandra I
authors: AI
authors: Jarmolinska
authors: Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.|Institute of Mathematics, University of Silesia, Bankowa 14, 40-007, Katowice, Poland.
authors: Wanda
authors: W
authors: Niemyska
authors: Department of Mathematics, University of St. Thomas, Saint Paul, MN 55105, USA.
authors: Eric J
authors: EJ
authors: Rawdon
authors: Department of Mathematics, University of California, Santa Barbara, CA 93106, USA.
authors: Kenneth C
authors: KC
authors: Millett
authors: Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland jsulkowska@chem.uw.edu.pl.|Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
authors: Joanna I
authors: JI
authors: Sulkowska
mesh_terms: D001704:Biopolymers; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D012984:Software; D013329:Structure-Activity Relationship; D064878:Web Browser
chemical_list: D001704:Biopolymers