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

Authors
  • Balabin, Ilya A
  • Hu, Xiangqian
  • Beratan, David N
Type
Published Article
Journal
Journal of computational chemistry
Publication Date
Mar 30, 2012
Volume
33
Issue
8
Pages
906–910
Identifiers
DOI: 10.1002/jcc.22927
PMID: 22298319
Source
Medline
License
Unknown

Abstract

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.

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