Knot_pull-python package for biopolymer smoothing and knot detection.
Bioinformatics
; 36(3): 953-955, 2020 02 01.
Article
en En
| MEDLINE
| ID: mdl-31504154
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_pull 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.
Texto completo:
1
Bases de datos:
MEDLINE
Asunto principal:
Programas Informáticos
/
Proteínas
Tipo de estudio:
Diagnostic_studies
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2020
Tipo del documento:
Article
País de afiliación:
Polonia