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Updated: May 25, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
Exploring biological electron transfer pathway dynamics with the Pathways plugin for VMD
Ilya A Balabin1, Xiangqian Hu, David N Beratan
1Department of Chemistry, Duke University, Durham, North Carolina 27708, USA. ilya.balabin@duke.edu
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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