Re: software/algorithm to cluster protein conformations

From: Joshua Adelman (
Date: Thu Apr 29 2010 - 18:06:38 CDT

Hi Basak,

You can probably use the gromacs tools:

There are other tools like MSMbuilder that has clustering functionality (built partially on gromacs tools):

For both of the above, you will need to convert the dcd file to either trr or xtc format. The former is possible using catdcd.

You could also use something like kmeans in matlab in combination with the matdcd tools. There are probably many other options that others can suggest.

Good luck.


On Apr 29, 2010, at 6:51 PM, Basak Isin wrote:

> Hello,
> I would like to cluster different conformations of a protein focusing on certain residues and their side chains. Is there any available softwares/algorithms that would perform this?
> Thanks much.
> Basak

Dr. Joshua L. Adelman
Postdoctoral Researcher - Grabe Lab
Department of Biological Sciences
University of Pittsburgh, Pittsburgh, PA

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