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Literature DB >> 29905836

KnotGenome: a server to analyze entanglements of chromosomes.

Joanna I Sulkowska^1,2, Szymon Niewieczerzal¹, Aleksandra I Jarmolinska^1,3, Jonathan T Siebert⁴, Peter Virnau⁴, Wanda Niemyska^1,5.

Abstract

The KnotGenome server enables the topological analysis of chromosome model data using three-dimensional coordinate files of chromosomes as input. In particular, it detects prime and composite knots in single chromosomes, and links between chromosomes. The knotting complexity of the chromosome is presented in the form of a matrix diagram that reveals the knot type of the entire polynucleotide chain and of each of its subchains. Links are determined by means of the Gaussian linking integral and the HOMFLY-PT polynomial. Entangled chromosomes are presented graphically in an intuitive way. It is also possible to relax structure with short molecular dynamics runs before the analysis. KnotGenome is freely available at http://knotgenom.cent.uw.edu.pl/.

Entities: Chemical Gene Species

Mesh：

Substances：
Polynucleotides

Year: 2018 PMID： 29905836 PMCID： PMC6030981 DOI： 10.1093/nar/gky511

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

23 in total

1. The fractal globule as a model of chromatin architecture in the cell.

Authors: Leonid A Mirny
Journal: Chromosome Res Date: 2011-01 Impact factor: 5.239

2. Conservation of complex knotting and slipknotting patterns in proteins.

Authors: Joanna I Sułkowska; Eric J Rawdon; Kenneth C Millett; Jose N Onuchic; Andrzej Stasiak
Journal: Proc Natl Acad Sci U S A Date: 2012-06-08 Impact factor: 11.205

3. Identification of rare slipknots in proteins and their implications for stability and folding.

Authors: Neil P King; Eric O Yeates; Todd O Yeates
Journal: J Mol Biol Date: 2007-08-02 Impact factor: 5.469

4. Topological knots and links in proteins.

Authors: Pawel Dabrowski-Tumanski; Joanna I Sulkowska
Journal: Proc Natl Acad Sci U S A Date: 2017-03-09 Impact factor: 11.205

5. LinkProt: a database collecting information about biological links.

Authors: Pawel Dabrowski-Tumanski; Aleksandra I Jarmolinska; Wanda Niemyska; Eric J Rawdon; Kenneth C Millett; Joanna I Sulkowska
Journal: Nucleic Acids Res Date: 2016-10-28 Impact factor: 16.971

6. PyLasso: a PyMOL plugin to identify lassos.

Authors: Aleksandra M Gierut; Wanda Niemyska; Pawel Dabrowski-Tumanski; Piotr Sulkowski; Joanna I Sulkowska
Journal: Bioinformatics Date: 2017-12-01 Impact factor: 6.937

7. Intricate knots in proteins: Function and evolution.

Authors: Peter Virnau; Leonid A Mirny; Mehran Kardar
Journal: PLoS Comput Biol Date: 2006-07-28 Impact factor: 4.475

8. Complex lasso: new entangled motifs in proteins.

Authors: Wanda Niemyska; Pawel Dabrowski-Tumanski; Michal Kadlof; Ellinor Haglund; Piotr Sułkowski; Joanna I Sulkowska
Journal: Sci Rep Date: 2016-11-22 Impact factor: 4.379

9. DNA knots occur in intracellular chromatin.

Authors: Antonio Valdés; Joana Segura; Sílvia Dyson; Belén Martínez-García; Joaquim Roca
Journal: Nucleic Acids Res Date: 2018-01-25 Impact factor: 16.971

10. 3D structures of individual mammalian genomes studied by single-cell Hi-C.

Authors: Tim J Stevens; David Lando; Srinjan Basu; Liam P Atkinson; Yang Cao; Steven F Lee; Martin Leeb; Kai J Wohlfahrt; Wayne Boucher; Aoife O'Shaughnessy-Kirwan; Julie Cramard; Andre J Faure; Meryem Ralser; Enrique Blanco; Lluis Morey; Miriam Sansó; Matthieu G S Palayret; Ben Lehner; Luciano Di Croce; Anton Wutz; Brian Hendrich; Dave Klenerman; Ernest D Laue
Journal: Nature Date: 2017-03-13 Impact factor: 49.962

3 in total