USING MODELLER IN WINDOWS

From Indipedia: India's Wikipedia at OSDD

Running Modeller in Windows:

MODELLER is a computer program that models protein 3D structure by satisfaction of spatial restraints.

MODELLER is most frequently used for homology or comparative protein structure modeling: The user provides an alignment of a sequence to be modeled with known related structures and MODELLER will automatically calculate an all-atom model.

To run the Modeller, we required three files related to our target protein and BLAST result. And these three files should be in a same folder and with same name. These files are-

With same name like- 1ZRL.atm

1ZRL.ali

1ZRL.py

1. Atom File preparation:-

To prepare the atom file we just require the atom file which is found in PDB(Protein Data Bank).

In PDB we enter a PDB id (like – 1ZRL)(which can known after the blast result of our target protein)

After entering the PDB id , we go to Display Files and open PDB File. With the help of this PDB File, we make our Atom File.

To make the atom file we just open this PDB File and simply copy from 1st ATOM to ending TER(as per your requirement, if there are more then one TER). (TER = terminator)

Example:

After copy this file on a notepad we have to delete the fifth column (as- A ). but the other column after coming 5th column should not be moved from their original position (only 5th column should be removed). Now your Atom file is ready to save it with .atm extension(1ZRL.atm) in a folder.

2. Alignment file preparation:- To preparation of Alignment file we required the Blast result of our target protein sequence, like -

Note:-

Query line is our target protein sequence and the Sbject line is the matched protein sequence from blast. So we check that our target protein sequence is complete or not in the query lines (do match to your query sequence with NCBI fasta format sequnece). If query sequence not match with fasta sequence, we write the atoms in query lines manually. It can be mismatch between the sequence line from any where.

In Alignment file, after checking the atoms we write these atoms in query lines and give the desks(-)in Sbject sequence line according to those atoms.

OR

Now your Alignment file is ready to save it with .ali extension(1ZRL.ali) in same folder in which atom file is present already.

3. Python file preparation:- Python file is just a program file in which we give the information of our atom file and alignment file and also give the information that how many structure we want to generate. Here is an example of python file, Please go through this program carefully.

from modeller.automodel import*

log.verbose()

env=environ()

env.io.atom_files_directory='./:../1ZRL.atm'

a=automodel(env,

alnfile='1ZRL.ali',

knowns='1ZRL',

sequence='SAT')

a.starting_model=1

a.ending_model=5

a.make()

Thus your python file is ready to run it & save it in .py extension (1ZRL.py) in same folder in which atom file and alignment file is present already.

On modeler command prompt, we give the path of our folder in which all three files are already presented and run 1ZRL.py (python) file only.