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KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers

  • Luca TubianaEmail author
  • Guido Polles
  • Enzo Orlandini
  • Cristian Micheletti
Open Access
Regular Article
First Online:
Part of the following topical collections:
  1. Advances in Computational Methods for Soft Matter Systems

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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Topical issue: Advances in Computational Methods for Soft Matter Systems 
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Acknowledgments

Open Access funding provided by University of Vienna.

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Copyright information

© The Author(s) 2018

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Authors and Affiliations

  • Luca Tubiana
    • 1
    Email author
  • Guido Polles
    • 2
  • Enzo Orlandini
    • 3
  • Cristian Micheletti
    • 4
  1. 1.Computational Physics DepartmentUniversity of ViennaViennaAustria
  2. 2.Molecular and Computational Biology, Department of Biological SciencesUniversity of Southern CaliforniaLos AngelesUSA
  3. 3.Dipartimento di Fisica e Astronomia and Sezione INFNUniversità di PadovaPadovaItaly
  4. 4.SISSAInternational School for Advanced StudiesTriesteItaly

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