I generated 1000 pdb structures of one protein, now want I to find a structure among these pdb files that have a helix conformer on defined amino acid (e.g., FGLN). How can I scan these files to find my structure?
Or it is better to say how can I use DSSP for multi pdb files (e.g. 1000)?
Hello Ramin,
In the case of DSSP you would have to write a script to automate the process. (2) You could also do the same using STRIDE stand alone or their web server. (3) Another option is to have the 1,000 files in the NMR PDB format. Just open and NMR with multiple structures from the PDB and you will see how they look like. Then you could use PROCHECK-NMR. It evaluates the quality of your structures. One of the results is the secondary structure that it plots schematically. (4) Another way is to submit this file (1,000 models) to the PDBSum server. (5) Finally, try the MOLPROBITY server. This is an excellent alternative protein models’ analysis and validity server. If you are not familiar with them, play a little bit with smaller files (5 to 10 models that you could prepare by hand) before doing the 1,000 models. These are just five ways of doing what you want. Good luck! Osmar.
Dear Osmar,
Thanks because of your detailed and kind instruction.
Ramin
you can use STRIDE, DSSP for ur use. the perl script (LINUX Machine) is :
@pdb=;
for($i=0;$i
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