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- Title
Knot_pull—python package for biopolymer smoothing and knot detection.
- Authors
Jarmolinska, Aleksandra I; Gambin, Anna; Sulkowska, Joanna I
- Abstract
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). Availability and implementation Knot_pull works under Python >=2.7 and is system independent. Source code and documentation are available at http://github.com/dzarmola/knot%5fpull under GNU GPL license and include also a wrapper script for PyMOL for easier visualization. Examples of smoothing trajectories can be found at: https://www.youtube.com/watch?v=IzSGDfc1vAY. Supplementary information Supplementary data are available at Bioinformatics online.
- Subjects
PYTHON programming language; SOURCE code; BIOPOLYMERS; PACKAGING; WRAPPERS
- Publication
Bioinformatics, 2020, Vol 36, Issue 3, p953
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btz644