Re: how to quantify and visualize the flow of water into a protein

From: Joshua Adelman (
Date: Tue Jul 08 2014 - 19:36:02 CDT

On Jul 8, 2014, at 7:20 PM, Thomas Evangelidis wrote:

> Greetings,
> Is anyone aware of any tool that helps visualize and/or quantify the flow of water into a transporter from an MD trajectory? I have a long trajectory of a transporter and want to find the main entrance points of water. I can see by manual inspection the various entrance points but it is difficult to decide which is/are the most important.
> thanks,
> Thomas
> --
> ======================================================================
> Thomas Evangelidis
> PhD student
> University of Athens
> Faculty of Pharmacy
> Department of Pharmaceutical Chemistry
> Panepistimioupoli-Zografou
> 157 71 Athens
> email:
> website:

Hi Thomas,

We recently published a paper looking at water permeation through the sugar transporter vSGLT:

We used a method wherein we constructed a network/graph based on the oxygen positions of all of the water molecules and then used Dijkstra's algorithm to enumerate the non-overlapping pathways through the network that cross from one side of the transporter to the other. Our system did not really have multiple entry points into the protein, but the method was useful for identifying sub-pathways that branched off of the main path. I could imagine then looking at the points where those pathways cross some continuous surface on the protein as a way of identifying entry points. Pathways could also probably be clustered to identify the dominant ones.

I have some python scripts that I could share if you want to contact me off list.


Dr. Joshua L. Adelman
Research Assistant Professor
Department of Biological Sciences
University of Pittsburgh, Pittsburgh, PA

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