[gmx-users] protein Aggregation using Gromacs

Ran Friedman r.friedman at bioc.uzh.ch
Wed May 12 09:30:05 CEST 2010


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

Good luck,

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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