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Helix at loop site

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Helix at loop site

Hi Dears,

I preformed using fragment-based loop modelling to model and get a 8 residue helix on the loop.
I generated 1000 models, now I want to filler my models to get a model with a helix on the loop,
Would you please let me know, how to find my mentioned model (i.e.,including a helix in loop area) among 1000 models.

Thanks in advance,

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Fri, 2013-05-31 07:04

I interpret your question to mean that you have a long loop which you think contains an 8-residue helix. You have 1000 models and want to know which, if any, have the secondary structure you need.

The simplest way to do this would be to use a DSSP tool to assign secondary structure for the protein and then search that database for structures with H in the desired region. For example, concatenate your DSSP assignments (labeled with file names) into one big file and write a script to sort the entries based on the number of "H" within the right range.

Rosetta is definitely capable of doing DSSP assignments, but I'm not sure that we have a boxed application that just takes input and reports DSSP. Writing yourself a quick script to do this in PyRosetta would be very simple; in pseudocode (this is not real code, but to give you an idea):

for (all PDBS)
load pdb into pose
print pose.dssp

You could combine it with a sorting script:

for (all PDBs):
load pdb into pose
string dssp = pose.dssp
int number_H

for thisposition in positions_in_loop:
if dssp[thisposition] == "H":

print dssp, number_H, posename

then sort the results on number_H.

Fri, 2013-05-31 08:13