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

Dabrowski-Tumanski, Pawel and Rubach, Pawel and Goundaroulis, Dimos and Dorier, Julien and Sułkowski, Piotr and Millett, Kenneth C. and Rawdon, Eric J. and Stasiak, Andrzej and Sulkowska, Joanna I. (2019) KnotProt 2.0: a database of proteins with knots and other entangled structures. Nucleic Acids Research, 47 (D1). D367-D375. ISSN 0305-1048. http://resolver.caltech.edu/CaltechAUTHORS:20181210-131132285

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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).


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1093/nar/gky1140DOIArticle
ORCID:
AuthorORCID
Dabrowski-Tumanski, Pawel0000-0001-9412-1716
Goundaroulis, Dimos0000-0002-2874-6272
Dorier, Julien0000-0002-6717-2451
Sułkowski, Piotr0000-0002-6176-6240
Stasiak, Andrzej0000-0002-0398-1989
Sulkowska, Joanna I.0000-0003-2452-0724
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.
Funders:
Funding AgencyGrant Number
National Science Centre (Poland)2012/07/E/NZ1/01900
National Science Centre (Poland)2016/21/N/NZ1/02848
Ministerstwo Nauki i Szkolnictwa Wyższego (MNiSW)0003/ID3/2016/64
NSFDMS-1418869
NSFDMS-1720342
European Research Council (ERC)335739
Leverhulme TrustRP2013-K-017
Swiss National Science Foundation (SNSF)31003A-166684
Record Number:CaltechAUTHORS:20181210-131132285
Persistent URL:http://resolver.caltech.edu/CaltechAUTHORS:20181210-131132285
Official Citation:Pawel Dabrowski-Tumanski, Pawel Rubach, Dimos Goundaroulis, Julien Dorier, Piotr Sułkowski, Kenneth C Millett, Eric J Rawdon, Andrzej Stasiak, Joanna I Sulkowska; KnotProt 2.0: a database of proteins with knots and other entangled structures, Nucleic Acids Research, Volume 47, Issue D1, 8 January 2019, Pages D367–D375, https://doi.org/10.1093/nar/gky1140
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:91645
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:10 Dec 2018 21:39
Last Modified:09 Jan 2019 17:46

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