ArticleThe European physical journal. E, Soft matter2018
KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers.
Article in The European physical journal. E, Soft matter, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Self-assembly Monte Carlo reveals localized entanglement in giant polymer melts.Nature communications · 2026Article
- In silico nanoscope to study the interplay of genome organization and transcription regulation.Nucleic acids research · 2025Article
- Unknotting RNA: A method to resolve computational artifacts.PLoS computational biology · 2025Article
- Unzipping of knotted DNA via nanopore translocation.QRB discovery · 2025Article
- Is There a Functional Role for the Knotted Topology in Protein UCH-L1?Journal of chemical information and modeling · 2024Article
- AlphaKnot 2.0: a web server for the visualization of proteins' knotting and a database of knotted AlphaFold-predicted models.Nucleic acids research · 2024Article
- Geometric learning of knot topology.Soft matter · 2023Article
- Knot Formation on DNA Pushed Inside Chiral Nanochannels.Polymers · 2023Article
- Topological Entanglement of Linear Catenanes: Knots and Threadings.ACS macro letters · 2023Article
- Long-lived metastable knots in polyampholyte chains.PloS one · 2023Article
- Geometric Predictors of Knotted and Linked Arcs.ACS polymers Au · 2022Article
- Knot Factories with Helical Geometry Enhance Knotting and Induce Handedness to Knots.Polymers · 2022Article
- Channels with Helical Modulation Display Stereospecific Sensitivity for Chiral Superstructures.Polymers · 2021Article
- Topoly: Python package to analyze topology of polymers.Briefings in bioinformatics · 2021Article
- Knot_pull-python package for biopolymer smoothing and knot detection.Bioinformatics (Oxford, England) · 2020Article
- Topical Issue on Dielectric Spectroscopy Applied to Soft Matter.The European physical journal. E, Soft matter · 2020Article
- Synergy of topoisomerase and structural-maintenance-of-chromosomes proteins creates a universal pathway to simplify genome topology.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Topical Issue on Advances in Computational Methods for Soft Matter Systems.The European physical journal. E, Soft matter · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The KymoKnot software package and web server identifies and locates physical knots or proper knots in a series of polymer conformations. It is mainly intended as an analysis tool for trajectories of linear or circular polymers, but it can be used on single instances too, e.g. protein structures in PDB format. A key element of the software package is the so-called minimally interfering chain closure algorithm that is used to detect physical knots in open chains and to locate the knotted region in both open and closed chains. The web server offers a user-friendly graphical interface that identifies the knot type and highlights the knotted region on each frame of the trajectory, which the user can visualize interactively from various viewpoints. The dynamical evolution of the knotted region along the chain contour is presented as a kymograph. All data can be downloaded in text format. The KymoKnot package is licensed under the BSD 3-Clause licence. The server is publicly available at http://kymoknot.sissa.it/kymoknot/interactive.php .
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.