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

Creators: Dabrowski-Tumanski, Pawel; Rubach, Pawel; Goundaroulis, Dimos; Dorier, Julien; Sułkowski, Piotr; Millett, Kenneth C.; Rawdon, Eric J.; Stasiak, Andrzej; Sulkowska, Joanna I.

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).

Additional Information

© The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Received: 15 September 2018; Revision Received: 24 October 2018; Accepted: 30 November 2018; Published: 01 December 2018. Funding: National Science Centre [2012/07/E/NZ1/01900 to J.I.S., 2016/21/N/NZ1/02848 to P.D.-T.]; ; Polish Ministry for Science and Higher Education Idea Plus Grant [0003/ID3/2016/64 to J.I.S.]; National Science Foundation [1418869 and 1720342 to E.J.R.]; ERC Starting Grant [335739] 'Quantum fields and knot homologies' funded by the European Research Council under the European Union's Seventh Framework Programme [to P.S.]; Leverhulme Trust [RP2013-K-017 to A.S.] ; Swiss National Science Foundation [31003A-166684 to A.S.]. Funding for open access charge: National Science Centre Grant. Conflict of interest statement. None declared.

Attached Files

Published - gky1140.pdf

Files

gky1140.pdf

Files (2.7 MB)

Name	Size	Download all
gky1140.pdf md5:c1ac6c3854bfa7bcfa3d398df8e8ab91	2.7 MB	Preview Download

Additional details

	All versions	This version
Views	0	0
Downloads	0	0
Data volume	0 Bytes	0 Bytes