Tracking single channel in protein dynamics


Beneš P., Medek P., Sochor J.


WSCG Communication Papers proceedings


In this paper we present a new approach to the processing of molecule dynamics. The method performs the tracking of a channel in a sequence of molecule snapshots which represent atom positions in the molecule in certain time intervals. The centerline of the tracked channel is refined using the Delaunay triangulation from the actual snapshot resulting in a new optimized centerline. This method allows us easily to animate the behaviour of the channel in the sequence. The method can also be used to detect the channel geometry in snapshots, where recent methods are not able to find this channel. In addition, the method yields information about channel parameters which vary over time. We can evaluate opening and closing of the input channel.


Beneš P., Medek P., Sochor J.: Tracking single channel in protein dynamics, WSCG Communication Papers proceedings, 109-114, 2010, ISBN 978-80-86943-87-9.
[BibTeX] [PDF]

sign in


Create new user account

Forgot your password? Please contact us at

user statistics

1219 citations
6071 registered users
111469x CAVER downloaded


CAVER was recently cited by the paper Structure of Escherichia coli cytochrome bd-II type oxidase...

Read more

CAVER was cited by the paper entitled Structural dynamics in the water and proton channels of...

Read more

November 2, 2021

CAVER was recently cited by the NATURE paper entitled Dispatched uses Na+flux to power release of...

Read more

other tools