Dears,
I run MD simulation on a transmembrane protein. When I visualised the frames, it seemed that I have some loss in alpha-helix (TM region). How can I quantify this?
NB: I used timeline of VMD to calculate the evolution of secondary structures during the simulation, but I need something else, more quantitatif..
What do you suggest, please?
Change in the secondary structure can be calculated in several ways. However, to make it easy for you, I would recommend you to use gmx_dssp tool if you performed your simulation in GROMACS. Please go through the following link to help yourself:
http://www.strodel.info/index_files/lecture/html/analysis.html
http://manual.gromacs.org/programs/gmx-do_dssp.html
http://www.mpibpc.mpg.de/266088/gmx_analysis
use -sc option and then go through the file that will provide you a direction to calculate the percentage of each secondary structure content.
Another option is to use VMD.
Article VMD-SS: A graphical user interface plug-in to calculate the ...
http://www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node256.html
Number of hydrogen bonds between protein backbone atoms.
This can be used along with the secondary structure to quantify the loss of helix population.
STRIDE web server is here:http://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py You can upload PDB file and simply count secondary structures assigned to residues.
You can try http://irdp.ncl.res.in/ as well..
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