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Exploring biological electron transfer pathway dynamics with the Pathways plugin for VMD.

Publication ,  Journal Article
Balabin, IA; Hu, X; Beratan, DN
Published in: Journal of computational chemistry
March 2012

We describe the new Pathways plugin for the molecular visualization program visual molecular dynamics. The plugin identifies and visualizes tunneling pathways and pathway families in biomolecules, and calculates relative electronic couplings. The plugin includes unique features to estimate the importance of individual atoms for mediating the coupling, to analyze the coupling sensitivity to thermal motion, and to visualize pathway fluctuations. The Pathways plugin is open source software distributed under the terms of the GNU's Not Unix (GNU) public license.

Duke Scholars

Published In

Journal of computational chemistry

DOI

EISSN

1096-987X

ISSN

0192-8651

Publication Date

March 2012

Volume

33

Issue

8

Start / End Page

906 / 910

Related Subject Headings

  • Software
  • Signal Transduction
  • Pseudomonas aeruginosa
  • Models, Molecular
  • Electron Transport
  • Computer Simulation
  • Chemical Physics
  • Bacterial Proteins
  • Azurin
  • 3407 Theoretical and computational chemistry
 

Citation

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MLA
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Balabin, I. A., Hu, X., & Beratan, D. N. (2012). Exploring biological electron transfer pathway dynamics with the Pathways plugin for VMD. Journal of Computational Chemistry, 33(8), 906–910. https://doi.org/10.1002/jcc.22927
Balabin, Ilya A., Xiangqian Hu, and David N. Beratan. “Exploring biological electron transfer pathway dynamics with the Pathways plugin for VMD.Journal of Computational Chemistry 33, no. 8 (March 2012): 906–10. https://doi.org/10.1002/jcc.22927.
Balabin IA, Hu X, Beratan DN. Exploring biological electron transfer pathway dynamics with the Pathways plugin for VMD. Journal of computational chemistry. 2012 Mar;33(8):906–10.
Balabin, Ilya A., et al. “Exploring biological electron transfer pathway dynamics with the Pathways plugin for VMD.Journal of Computational Chemistry, vol. 33, no. 8, Mar. 2012, pp. 906–10. Epmc, doi:10.1002/jcc.22927.
Balabin IA, Hu X, Beratan DN. Exploring biological electron transfer pathway dynamics with the Pathways plugin for VMD. Journal of computational chemistry. 2012 Mar;33(8):906–910.
Journal cover image

Published In

Journal of computational chemistry

DOI

EISSN

1096-987X

ISSN

0192-8651

Publication Date

March 2012

Volume

33

Issue

8

Start / End Page

906 / 910

Related Subject Headings

  • Software
  • Signal Transduction
  • Pseudomonas aeruginosa
  • Models, Molecular
  • Electron Transport
  • Computer Simulation
  • Chemical Physics
  • Bacterial Proteins
  • Azurin
  • 3407 Theoretical and computational chemistry