Journal
NUCLEIC ACIDS RESEARCH
Volume 43, Issue D1, Pages D306-D314Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gku1059
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Funding
- National Science Center [2012/07/E/NZ1/01900]
- European Molecular Biology Organization [2757/2014]
- Foundation for Polish Science [177/UD/SKILLS/2012, TEAM/2011-7/6]
- Ministry of Science and Higher Education
- National Science Foundation [Division of Mathematical Sciences] [1115722, 1418869]
- Swiss National Foundation [31003A_138267]
- The Leverhulme Trust [RP2013-K-017]
- Division Of Mathematical Sciences
- Direct For Mathematical & Physical Scien [1115722] Funding Source: National Science Foundation
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The protein topology database KnotProt, ext-link-type=uri xlink:href=http://knotprot.cent.uw.edu.pl/ xlink:type=simple>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.
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