Title

Authors

Affiliation

Biotechnology Division, Central Institute of Medicinal and Aromatic Plants, (Council of Scientific and Industrial Research), Kukrail Picnik Spot Road, P.O. CIMAP, Lucknow - 226015, India

Email

roysudeep28@gmail.com; *Corresponding author

Phone

+919450614880

Article Type

Hypothesis

Date

Received June 18, 2011; Accepted June 27, 2011; Published July 06, 2011

Various species of Ocimum have acquired special attention due to their medicinal properties. Different parts of the plant (root, stem, flower, leaves) are used in the treatment of a wide range of disorders from centuries. Experimental structures (X-ray and NMR) of proteins from different Ocimum species, are not yet available in the Protein Databank (PDB). These proteins play a key role in various metabolic pathways in Ocimum. 3D structures of the proteins are essential to determine most of their functions. Homology modeling approach was employed in order to derive structures for these proteins. A program meant for comparative modeling- Modeller 9v7 was utilized for the purpose. The modeled proteins were further validated by Prochek and Verify-3d and Errat servers. Amino acid composition and polarity of these proteins was determined by CLC-Protein Workbench tool. Expasy’s Prot-param server and Cys_rec tool were used for physico-chemical and functional characterization of these proteins. Studies of secondary structure of these proteins were carried out by computational program, Profunc. Swiss-pdb viewer was used to visualize and analyze these homology derived structures. The structures are finally submitted in Protein Model Database, PMDB so that they become accessible to other users for further studies.

Keywords

Ocimum, Homology modeling, CLC protein work bench, Secondary structure prediction, Swiss-PDB Viewer

Citation

Roy et al. Bioinformation 6(8): 315-319 (2011)
 

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.