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

Pawel Dabrowski-Tumanski; Pawel Rubach; Dimos Goundaroulis; Julien Dorier; Piotr Sukowski; Kenneth C. Millett; Eric J. Rawdon; Andrzej Stasiak; Joanna I. Sulkowska

doi:10.1093/nar/gky1140

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

Pawel Dabrowski-Tumanski
, Pawel Rubach
, Dimos Goundaroulis
, Julien Dorier
, Piotr Sukowski
, Kenneth C. Millett
, Eric J. Rawdon
, Andrzej Stasiak
, Joanna I. Sulkowska

Research output: Contribution to journal › Article › peer-review

97 Scopus citations

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).

Original language	English (US)
Pages (from-to)	D367-D375
Journal	Nucleic acids research
Volume	47
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gky1140
State	Published - 2019
Externally published	Yes

ASJC Scopus subject areas

Genetics

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10.1093/nar/gky1140

Cite this

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title = "KnotProt 2.0: A database of proteins with knots and other entangled structures",

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).",

author = "Pawel Dabrowski-Tumanski and Pawel Rubach and Dimos Goundaroulis and Julien Dorier and Piotr Sukowski and Millett, \{Kenneth C.\} and Rawdon, \{Eric J.\} and Andrzej Stasiak and Sulkowska, \{Joanna I.\}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.",

year = "2019",

doi = "10.1093/nar/gky1140",

language = "English (US)",

volume = "47",

pages = "D367--D375",

journal = "Nucleic acids research",

issn = "0305-1048",

publisher = "Oxford University Press",

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T2 - A database of proteins with knots and other entangled structures

AU - Dabrowski-Tumanski, Pawel

AU - Rubach, Pawel

AU - Goundaroulis, Dimos

AU - Dorier, Julien

AU - Sukowski, Piotr

AU - Millett, Kenneth C.

AU - Rawdon, Eric J.

AU - Stasiak, Andrzej

AU - Sulkowska, Joanna I.

PY - 2019

Y1 - 2019

N2 - 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).

AB - 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).

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DO - 10.1093/nar/gky1140

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JO - Nucleic acids research

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ER -

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

Abstract

ASJC Scopus subject areas

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