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

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  • Open Access
  • Published: 07 June 2018
  • volume 41, Article number: 72 (2018)
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KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers
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  • Luca Tubiana1,
  • Guido Polles2,
  • Enzo Orlandini3 &
  • …
  • Cristian Micheletti4 

  • 865 Accesses

  • 34 Citations

  • 2 Altmetric

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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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Acknowledgments

Open Access funding provided by University of Vienna.

Author information

Authors and Affiliations

  1. Computational Physics Department, University of Vienna, Sensengasse 8/10, 1090, Vienna, Austria

    Luca Tubiana

  2. Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, 90089, Los Angeles, CA, USA

    Guido Polles

  3. Dipartimento di Fisica e Astronomia and Sezione INFN, Università di Padova, Via Marzolo 8, 35131, Padova, Italy

    Enzo Orlandini

  4. SISSA, International School for Advanced Studies, Via Bonomea 265, I-34136, Trieste, Italy

    Cristian Micheletti

Authors
  1. Luca Tubiana
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  2. Guido Polles
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  4. Cristian Micheletti
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Correspondence to Luca Tubiana.

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Tubiana, L., Polles, G., Orlandini, E. et al. KymoKnot: A web server and software package to identify and locate knots in trajectories of linear or circular polymers. Eur. Phys. J. E 41, 72 (2018). https://doi.org/10.1140/epje/i2018-11681-0

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  • Received: 15 February 2018

  • Accepted: 18 May 2018

  • Published: 07 June 2018

  • DOI: https://doi.org/10.1140/epje/i2018-11681-0

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Keywords

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

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