Homology modeling of protein using Modeller Software

Homology modeling using Modeller software

Step 1: Installing Modeller Software

Download and install latest version of  Modeller software: http://salilab.org/modeller/download_installation.html
After registration, you will get an academic licence for installation.

Step 2: Download and install python: http://www.python.org/download/releases/2.4/

Step 3: Paste your raw protein sequence and search against pdb database using BLASTP program
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome

Note: Choose database search set as protein data bank (pdb). find the best template hit. The template hit should have atleast greater than 35% of identity. Note down the pdb id (Eg:1BDM).

Step 4: Now download the pdb file from pdb database: http://www.rcsb.org/pdb/home/home.do


Step 5: Go to C:\\Program Files\Modeller folder\

Now, copy the downloaded pdb file in modeller folder. Now rename the pdb file name as "1bdm.pdb"

Step 6: Now, open new notepad file, copy and paste the following program
>P1;TvLDH
sequence:TvLDH:::::::0.00: 0.00
MSEAAHVLITGAAGQIGYILSHWIASGELYGDRQVYLHLLDIPPAMNRLTALTMELEDCAFPHLAGFVATTDPKA
AFKDIDCAFLVASMPLKPGQVRADLISSNSVIFKNTGEYLSKWAKPSVKVLVIGNPDNTNCEIAMLHAKNLKPEN
FSSLSMLDQNRAYYEVASKLGVDVKDVHDIIVWGNHGESMVADLTQATFTKEGKTQKVVDVLDHDYVFDTFFKKI
GHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPVPEGNPYGIKPGVVFSFPCNVDKEGKIHVV
EGFKVNDWLREKLDFTEKDLFHEKEIALNHLAQGG*
Now, replace the existing sequence with your sequence. Only, sequence has to be replaced. Now, save the notepad file as "TvLDH.ali". Give the file name within the double quote.

Step 7: Now, open new notepad file, copy and paste the following program


from modeller import *
env = environ()
aln = alignment(env)
mdl = model(env, file='1bdm', model_segment=('FIRST:A','LAST:A'))
aln.append_model(mdl, align_codes='1bdmA', atom_files='1bdm.pdb')
aln.append(file='TvLDH.ali', align_codes='TvLDH')
aln.align2d()
aln.write(file='TvLDH-1bdmA.ali', alignment_format='PIR')
aln.write(file='TvLDH-1bdmA.pap', alignment_format='PAP')

Now, save the notepad file as "align.py". Give the file name within the double quote. It will automatically changed into python format.
Now, run the "align.py" by double clicking it. It will run now and create 'TvLDH-1bdmA.ali' and 'TvLDH-1bdmA.pap' file. Depend on the sequence length, it will take time to complete.

Step 8: Now, open new notepad file, copy and paste the following program

from modeller import *
from modeller.automodel import *
env = environ()
a = automodel(env, alnfile='TvLDH-1bdmA.ali',
              knowns='1bdmA', sequence='TvLDH',
              assess_methods=(assess.DOPE, assess.GA341))
a.starting_model = 1
a.ending_model = 5
a.make()

Now, save the notepad file as "model.py". Give the file name within the double quote.
Run the "model.py" file by double clicking it. It will run and generate 5 pdb model.


Now check the model efficiency and accurecy by validating it. Go to SAVES server. http://nihserver.mbi.ucla.edu/SAVES/. upload the modelled pdb file, and run all the program.

Check the ramachandran plot value (should be greater than 95%) and errat value (should be great then 90%). If it is less, Do model optimization, energy minimization and protein (molecular dynamics) simulation.