[modeller_usage] Homology modelling a loop

[Anjela Manandhar <anjelamanandhar@gmail.com>]

Hello,

I need to model a missing loop for my protein. I used the sequence of missing loop and aligned with its homologous sequence. Then I modeled my loop from the alignment. Now the problem is my modeled loop is very far away from the place where it needs to be ( due to the template i used). So how can I stitch my loop into the protein. Also, is there a way to homology model the loop such that its position is within the protein.

I am attaching my script and alignment files.

Sincerely,

Anjela Manandhar

Graduate Student

Biochemistry Program

Graduate Center, City University of New York

365 Fifth Avenue, NY-10016, USA

Attachment: loop.ali
Description: Binary data

from modeller import *
from modeller.automodel import *
#from modeller import soap_protein_od

env = environ()
a = loopmodel(env, alnfile='H1-B2.ali',
              knowns='1JFFB', sequence='loop',
              #inifile='mymodel.pdb',
              assess_methods=(assess.DOPE,
                              #soap_protein_od.Scorer(),
                              assess.GA341))
a.starting_model = 1
a.ending_model = 20
a.make()

from modeller import *

env = environ()
aln = alignment(env)
mdl = model(env, file='1JFF', model_segment=('35:B','60:B'))
aln.append_model(mdl, align_codes='1JFFB', atom_files='1JFF.pdb')
aln.append(file='loop.ali', align_codes='loop')
aln.align2d()
aln.write(file='H1-B2.ali', alignment_format='PIR')
aln.write(file='H1-B2.pap', alignment_format='PAP')

Attachment: H1-B2.ali
Description: Binary data