KnotProt: a database of proteins with knots and slipknots
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.
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.Attached Files
Published - Nucl._Acids_Res.-2015-Jamroz-D306-14.pdf
Files
Name | Size | Download all |
---|---|---|
md5:d7d8366c451793d4a82a28e2bdcde6a9
|
1.9 MB | Preview Download |
Additional details
- PMCID
- PMC4383900
- Eprint ID
- 51488
- Resolver ID
- CaltechAUTHORS:20141110-092257146
- 2012/07/E/NZ1/01900
- National Science Centre (Poland)
- 2757/2014
- European Molecular Biology Organization (EMBO)
- Foundation for Polish Science
- Ministry of Science and Higher Education (Poland)
- DMS-1115722
- NSF
- DMS-1418869
- NSF
- 31003A 138267
- Swiss National Foundation (SNF)
- RP2013-K-017
- Leverhulme Trust
- Created
-
2014-11-10Created from EPrint's datestamp field
- Updated
-
2021-11-10Created from EPrint's last_modified field