Hi 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 <[email protected]> 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: [email protected] > 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 > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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