KnotProt 2.0: a database of proteins with knots and other entangled structures

Pawel Dabrowski-Tumanski; Pawel Rubach; Dimos Goundaroulis; Julien Dorier; Piotr Sulkowski; Kenneth C Millett; Eric J Rawdon; Andrzej Stasiak; Joanna I Sulkowska

doi:10.1093/nar/gky1140

KnotProt 2.0: a database of proteins with knots and other entangled structures

Nucleic Acids Res. 2019 Jan 8;47(D1):D367-D375. doi: 10.1093/nar/gky1140.

Authors

Pawel Dabrowski-Tumanski^{1

2}, Pawel Rubach^{2

3}, Dimos Goundaroulis⁴, Julien Dorier⁵, Piotr Sulkowski^{6

7}, Kenneth C Millett⁸, Eric J Rawdon⁹, Andrzej Stasiak⁴, Joanna I Sulkowska^{1

2}

Affiliations

¹ Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, Poland.
² Centre of New Technologies, University of Warsaw, Banacha 2c, Warsaw, Poland.
³ Warsaw School of Economics, Al. Niepodlegosci 162, Warsaw, Poland.
⁴ Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
⁵ Vital-IT, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
⁶ Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw, Poland.
⁷ Walter Burke Institute for Theoretical Physics, California Institute of Technology, Pasadena, CA 91125, USA.
⁸ Department of Mathematics, University of California, Santa Barbara, CA 93106, USA.
⁹ Department of Mathematics, University of St. Thomas, Saint Paul, MN 55105, USA.

Abstract

The KnotProt 2.0 database (the updated version of the KnotProt database) collects information about proteins which form knots and other entangled structures. New features in KnotProt 2.0 include the characterization of both probabilistic and deterministic entanglements which can be formed by disulfide bonds and interactions via ions, a refined characterization of entanglement in terms of knotoids, the identification of the so-called cysteine knots, the possibility to analyze all or a non-redundant set of proteins, and various technical updates. The KnotProt 2.0 database classifies all entangled proteins, represents their complexity in the form of a knotting fingerprint, and presents many biological and geometrical statistics based on these results. Currently the database contains >2000 entangled structures, and it regularly self-updates based on proteins deposited in the Protein Data Bank (PDB).

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Animals
Cysteine / chemistry
Cystine / chemistry
Data Management
Databases, Protein*
Humans
Ions / chemistry
Models, Molecular*
Probability
Protein Conformation*
Protein Folding
User-Computer Interface

Substances

Ions
Cystine
Cysteine