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Nucleic Acids Res. 2017 Jan 4;45(D1):D243-D249. doi: 10.1093/nar/gkw976. Epub 2016 Oct 28.

LinkProt: a database collecting information about biological links.

Author information

1
Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.
2
Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
3
College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland.
4
Institute of Mathematics, University of Silesia, Bankowa 14, 40-007, Katowice, Poland.
5
Department of Mathematics, University of St. Thomas, Saint Paul, MN 55105, USA.
6
Department of Mathematics, University of California, Santa Barbara, CA 93106, USA.
7
Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland jsulkowska@chem.uw.edu.pl.

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.

PMID:
27794552
PMCID:
PMC5210653
DOI:
10.1093/nar/gkw976
[Indexed for MEDLINE]
Free PMC Article

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