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KnotProt: a database of proteins with knots and slipknots

Jamroz, Michal and Niemyska, Wanda and Rawdon, Eric J. and Stasiak, Andrzej and Millett, Kenneth C. and Sułkowski, Piotr and Sulkowska, Joanna I. (2015) KnotProt: a database of proteins with knots and slipknots. Nucleic Acids Research, 43 (D1). D306-D314. ISSN 0305-1048. PMCID PMC4383900. https://resolver.caltech.edu/CaltechAUTHORS:20141110-092257146

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Abstract

The protein topology database KnotProt, http://knotprot.cent.uw.edu.pl/, collects information about protein structures with open polypeptide chains forming knots or slipknots. The knotting complexity of the cataloged proteins is presented in the form of a matrix diagram that shows users the knot type of the entire polypeptide chain and of each of its subchains. The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot’s core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot. In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting. As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprints.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1093/nar/gku1059DOIArticle
http://nar.oxfordjournals.org/content/43/D1/D306PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383900/PubMed CentralArticle
ORCID:
AuthorORCID
Stasiak, Andrzej0000-0002-0398-1989
Sułkowski, Piotr0000-0002-6176-6240
Sulkowska, Joanna I.0000-0003-2452-0724
Additional Information:© The Author(s) 2014. 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 August 15, 2014. Revision received October 10, 2014. Accepted October 15, 2014. First published online: October 31, 2014. We acknowledge the support of the StackOverflow community. Funding: National Science Center [2012/07/E/NZ1/01900 to J.S.]; European Molecular Biology Organization [Installation Grant #2757/2014 to J.S.]; Foundation for Polish Science [Homing Plus to J.S., SKILLS/Inter 177/UD/SKILLS/2012 to P.S., TEAM TEAM/2011-7/6 to M.J.]; Ministry of Science and Higher Education [Iuventus Plus programme to P.S.]; National Science Foundation [Division of Mathematical Sciences, #1115722 and # 1418869 to E.R.]; Swiss National Foundation [31003A 138267 to A.S.] and The Leverhulme Trust [RP2013-K-017 to A.S.]. Funding for open access charge: Swiss National Foundation [31003A 138267]. Conflict of interest statement. None declared.
Funders:
Funding AgencyGrant Number
National Science Centre (Poland)2012/07/E/NZ1/01900
European Molecular Biology Organization (EMBO)2757/2014
Foundation for Polish ScienceUNSPECIFIED
Ministry of Science and Higher Education (Poland)UNSPECIFIED
NSFDMS-1115722
NSFDMS-1418869
Swiss National Foundation (SNF)31003A 138267
Leverhulme TrustRP2013-K-017
Issue or Number:D1
PubMed Central ID:PMC4383900
Record Number:CaltechAUTHORS:20141110-092257146
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20141110-092257146
Official Citation:Michal Jamroz, Wanda Niemyska, Eric J. Rawdon, Andrzej Stasiak, Kenneth C. Millett, Piotr Sułkowski, and Joanna I. Sulkowska KnotProt: a database of proteins with knots and slipknots Nucl. Acids Res. (28 January 2015) 43 (D1): D306-D314 first published online October 31, 2014 doi:10.1093/nar/gku1059
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:51488
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:10 Nov 2014 17:35
Last Modified:09 Mar 2020 13:19

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