KnotProt 2.0: a database of proteins with knots and other entangled structures
Open Access
- 1 December 2018
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 47 (D1), D367-D375
- https://doi.org/10.1093/nar/gky1140
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).Funding Information
- National Science Centre (2012/07/E/NZ1/01900, 2016/21/N/NZ1/02848)
- Polish Ministry for Science and Higher Education Idea Plus (0003/ID3/2016/64)
- National Science Foundation (1418869, 1720342)
- European Research Council (335739)
- Leverhulme Trust (RP2013-K-017)
- Swiss National Science Foundation (31003A-166684)
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