Hello,

I used Modeller to reconstruct around a 100 proteins with true residue-residue contacts and secondary structure information. I could reconstruct only a few proteins with high accuracy. Below is a sample script I used for Modelling. I did not use any templates. (I found that Modeller satisfies more contact restraints when I provided a template with just one residue’s coordinates instead of an extended structure as a template.) I wonder why Modeller could not satisfy true contact restraints. Is there any specific way to reconstruct proteins using true residue contacts?

My PY files and PIR files look like this:

from modeller import *

from modeller.automodel import *

log.verbose()

env = environ()

env.io.atom_files_directory = ['.']

class MyModel(automodel):

def special_restraints(self, aln):

rsr = self.restraints

at = self.atoms

# Helices and Strands

rsr.add(secondary_structure.strand(self.residue_range('3:', '11:')))

rsr.add(secondary_structure.strand(self.residue_range('16:', '26:')))

rsr.add(secondary_structure.alpha(self.residue_range('126:', '140:')))

# Contacts:

rsr.add(forms.upper_bound(group=physical.xy_distance,feature=features.distance(at['CA:9'], at['CA:18']),mean=8.0, stdev=0.1))

rsr.add(forms.upper_bound(group=physical.xy_distance,feature=features.distance(at['CB:3'], at['CB:24']),mean=8.0, stdev=0.1))

rsr.add(forms.upper_bound(group=physical.xy_distance,feature=features.distance(at['CB:5'], at['CB:22']),mean=8.0, stdev=0.1))

rsr.add(forms.upper_bound(group=physical.xy_distance,feature=features.distance(at['CB:122'], at['CB:132']),mean=8.0, stdev=0.1))

a = MyModel(env,

alnfile = '1f21.pir', # alignment filename

knowns = 'empty', # codes of the templates

sequence = '1f21') # code of the target

a.starting_model= 1

a.ending_model = 20

a.make()

C;

>P1;empty

structureX:empty: 1: : 152: : : :1.0:

K-------------------------------------------------------------------------------------------------------------------------------------------------------*

C;

>P1;1f21

: : : : : : : : :

KQVEIFTDGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHAEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKGHAGHPENERADELARAAAMNPTLEDTGYQVE*

Badri Adhikari

University of Missouri