Exploring biological electron transfer pathway dynamics with the Pathways plugin for VMD.
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.
Department of Chemistry, Duke University, Durham, North Carolina 27708, USA. ilya.balabin@duke.edu
Ilya A
IA
Balabin
Xiangqian
X
Hu
David N
DN
Beratan
D001400:Azurin / Q000737:chemistry*; D001426:Bacterial Proteins / Q000737:chemistry*; D003198:Computer Simulation; D004579:Electron Transport; D008958:Models, Molecular; D011550:Pseudomonas aeruginosa / Q000737:chemistry*; D015398:Signal Transduction; D012984:Software
D001426:Bacterial Proteins; D001400:Azurin