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ABSTRACT   REFERENCES  
Journal of Bioinformatics and Research 1(2-3) 2012: 36-40

Python Program to Generate Atom Records from PDB Protein Files for Drug Design Studies


Srinivasu Nulaka1*, Appa Rao Allam2, Suresh Kopparthi3

1Department of Computer Science (MCA), KGRL College, Bhimavaram, Andhra Pradesh, India.
2Former Vice-chancellor, JNTUK, Kakinada, Andhra Pradesh, India.
3Department of Computer Science, MP College of Engg & Tech , Bhimavaram, Andhra Pradesh, India.

* To whom correspondence should be addressed. Email: nulaka@gmail.com

ABSTRACT

Protein data bank is the major repository source of macromolecule 3-dimensional files in varied formats such as .ent,
.pdb, .xml, .mmcif etc. The most widely used format is .ent and .pdb by many drug design experts in various computeraided
studies. The major requirement for any drug design or docking study is 3D format of protein as input without any
heteroatoms. Other soft wares perform the task of separating protein and heteroatoms from PDB file, however, they
require manual intervention. Therefore, a python based program was reported here that takes 3-dimensional PDB file
as input and returns a file with only ATOM records in it. This output file is more important as an input in docking or
protein-ligand interaction studies. The lines of python code were given in the manuscript.


Copyright © 2012 | AIZEON publishers | All rights reserved

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Citation: Nulaka S, Allam AR and Kopparthi S (2012). Python Program to Generate Atom Records from PDB Protein Files for Drug Design Studies. Journal of Bioinformatics and Research 1(2-3): 36-40

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