[gmx-users] protein Aggregation using Gromacs
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 listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein Aggregation using Gromacs
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. +41-44-639 Email: r.fried...@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 -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein Aggregation using Gromacs
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 r.fried...@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. +41-44-639 Email: r.fried...@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 -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] protein Aggregation using Gromacs
Hello again - IMHO the best approach for any simulation study is to plan how the simulation will be used to solve a specific scientific problem before running the simulations, rather then the other way around. To clarify what I wrote below, there's no algorithm I'm aware of where the input is an MD simulation of a certain protein and the output is an aggregation propensity of certain residues. Having said that, simulations can be a useful tool to study amyloid aggregation and even tendency of specific residues to aggregate first. A useful approach was developed in the group where I work now, based on the aggregation propensity of peptide sequences decomposed from the whole protein: http://dx.doi.org/10.1016/j.jmb.2006.01.009 Using your simulations, you can check if some residues are more prone to lose their secondary structure as the temperature increases, which suggests that they are more likely to unfold. Do bear in mind though that aggregation is a complex process which involves multimers. Unless you show some correlation with experimental findings it will be difficult to defend your conclusions. Ran shahid nayeem wrote: 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* r.fried...@bioc.uzh.ch mailto:r.fried...@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. +41-44-639 Email: r.fried...@bioc.uzh.ch mailto:r.fried...@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 -- gmx-users mailing listgmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
