[gmx-users] protein Aggregation using Gromacs

shahid nayeem msnayeem at gmail.com
Wed May 12 12:05:23 CEST 2010

 I have used TANGO Aggrescan, Zyggregator and other online tools but I am
unable to find and pinpoint residue responsible for aggregation. Then I did
MD simulation of the proteins with gromacs at different temperature. Now in
this background I need  suggestion to analyse my MD trajectory.
shahid Nayeem

On 5/12/10, Ran Friedman <r.friedman at bioc.uzh.ch> wrote:
> Hi,
> There's no recipie to locate aggregation hot spots based on MD
> simulations. There are many papers on simulations of protein and peptide
> aggregation from which you can draw some ideas, but bear in mind that
> aggregation of more than very few and very small peptides is typically
> much slower than what one can simulate using atomistic MD.
> For a quick approach you can use sequence analysis tools, e.g., TANGO
> http://tango.crg.es/
> Good luck,
> Ran
> --
> ------------------------------------------------------
> Ran Friedman
> Postdoctoral Fellow
> Computational Structural Biology Group (A. Caflisch)
> Department of Biochemistry
> University of Zurich
> Winterthurerstrasse 190
> CH-8057 Zurich, Switzerland
> Tel. +41-44-6355559
> Email: r.friedman at bioc.uzh.ch
> Skype: ran.friedman
> ------------------------------------------------------
> shahid nayeem wrote:
> > Dear all
> > What are the analysis tools which should be used on MD trajectory file
> > in order to find potential aggregation sites of a protein. Anyone can
> > tell me about specific resource material on use of Gromacs to predict
> > protein aggregation hot spots from MD trajectory anlysis.
> > Shahid Nayeem
> --
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