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

被引：74

作者：

Dabrowski-Tumanski, Pawel ^{[1
,2
]}

Rubach, Pawel ^{[2
,3
]}

Goundaroulis, Dimos ^{[4
,5
]}

Dorier, Julien ^{[6
]}

Sulkowski, Piotr ^{[7
,8
]}

Millett, Kenneth C. ^{[9
]}

Rawdon, Eric J. ^{[10
]}

Stasiak, Andrzej ^{[4
,5
]}

Sulkowska, Joanna I. ^{[1
,2
]}

机构：

[1] Univ Warsaw, Fac Chem, Pasteura 1, Warsaw, Poland

[2] Univ Warsaw, Ctr New Technol, Banacha 2c, Warsaw, Poland

[3] Warsaw Sch Econ, Al Niepodlegosci 162, Warsaw, Poland

[4] Univ Lausanne, Ctr Integrat Genom, CH-1015 Lausanne, Switzerland

[5] SIB Swiss Inst Bioinformat, CH-1015 Lausanne, Switzerland

[6] SIB Swiss Inst Bioinformat, Vital IT, CH-1015 Lausanne, Switzerland

[7] Univ Warsaw, Fac Phys, Pasteura 5, Warsaw, Poland

[8] CALTECH, Walter Burke Inst Theoret Phys, Pasadena, CA 91125 USA

[9] Univ Calif Santa Barbara, Dept Math, Santa Barbara, CA 93106 USA

[10] Univ St Thomas, Dept Math, St Paul, MN 55105 USA

来源：

NUCLEIC ACIDS RESEARCH | 2019年 / 47卷 / D1期

基金：

瑞士国家科学基金会; 欧洲研究理事会; 美国国家科学基金会;

关键词：

PLANT CYCLOTIDES; CYSTINE; STABILITY; PEPTIDES; FAMILY;

D O I：

10.1093/nar/gky1140

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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).

引用

页码：D367 / D375

页数：9

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