Premium
Exploring biological electron transfer pathway dynamics with the Pathways Plugin for VMD
Author(s) -
Balabin Ilya A.,
Hu Xiangqian,
Beratan David N.
Publication year - 2012
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.22927
Subject(s) - plug in , visualization , computer science , coupling (piping) , license , programming language , data mining , operating system , materials science , metallurgy
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. © 2012 Wiley Periodicals, Inc.