Table of Contents
Journal of Viruses
Volume 2014, Article ID 752656, 6 pages
http://dx.doi.org/10.1155/2014/752656
Research Article

Recognition of Errors in the Refinement and Validation of Three-Dimensional Structures of AC1 Proteins of Begomovirus Strains by Using ProSA-Web

Department of Science, Faculty of Arts, Science and Commerce, Mody Institute of Technology and Science, Lakshmangarh, Sikar, Rajasthan 332311, India

Received 22 June 2013; Revised 2 October 2013; Accepted 2 October 2013; Published 2 January 2014

Academic Editor: Sílvia Bofill-Mas

Copyright © 2014 Rajneesh Prajapat et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

The structural model of begomovirus AC1 protein is useful for understanding biological function at molecular level and docking study. For this study we have used the ProSA program (Protein Structure Analysis) tool to establish the structure prediction and modeling of protein. This tool was used for refinement and validation of experimental protein structures. Potential problems of protein structures based on energy plots are easily seen by ProSA and are displayed in a three-dimensional manner. In the present study we have selected different AC1 proteins of begomovirus strains (YP_003288785, YP_002004579, and YP_003288773) for structural analysis and display of energy plots that highlight potential problems spotted in protein structures. The 3D models of Rep proteins with recognized errors can be effectively used for in silico docking study for development of potential ligand molecules against begomovirus infection.