4.7 Article

Knot_pull-python package for biopolymer smoothing and knot detection

Journal

BIOINFORMATICS
Volume 36, Issue 3, Pages 953-955

Publisher

OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btz644

Keywords

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Funding

  1. National Science Centre [2018/29/N/NZ2/02897, 2018/29/B/ST6/00681]
  2. Polish Ministry for Science and Higher Education [0003/ID3/2016/64]
  3. EMBO YIP

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A Summary: 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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