Knot_pull—python package for biopolymer smoothing and knot detection | Zendy

Aleksandra I. Jarmolinska | Zendy; Anna Gambin | Zendy; Joanna I. Sułkowska | Zendy

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Knot_pull—python package for biopolymer smoothing and knot detection

Author(s) -

Aleksandra I. Jarmolinska,

Anna Gambin,

Joanna I. Sułkowska

Publication year - 2019

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btz644

Subject(s) - python (programming language) , computer science , knot (papermaking) , mit license , visualization , smoothing , computer graphics (images) , programming language , trefoil knot , documentation , source code , theoretical computer science , software , data mining , computer vision , knot theory , engineering , chemical engineering

The biggest hurdle in studying topology in biopolymers is the steep learning curve for actually seeing the knots in structure visualization. Knot_pull is a command line utility designed to simplify this process-it presents the user with a smoothing trajectory for provided structures (any number and length of protein, RNA or chromatin chains in PDB, CIF or XYZ format), and calculates the knot type (including presence of any links, and slipknots when a subchain is specified).

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