Three dimensional structure modeling and ramachandran plot analysis of autographa californica nucleopolyhdro viral protein

Abstract

Background: Autographa Californica's nucleopolyhedro is a viral protein found in baciloviridae. It is made of double stranded DNA genome. They viral protein easily infects this insect and affects the expression system. Method: The main aim of this work is to predict various viral proteins (Autographa Californica nucleopolyhedro). FASTA sequences are retrived from NCBI (National Center for Biotechnology Information) database. Then Basic Local Alignment Search Tool (BLAST) used to find regions of similarity in different sequences. The homology modeling was done in swiss model. The template model also constructed. Results: Comparative modeling of this program to predict the protein sequence identity is 46.83%.The template protein e value is 110 and they chain A having identify 100% similarity maximum score 320.Further the protein structure was validated in Ramachandran plot. Conclusion: From Ramachandran plot analysis it was found that the portions of residues falling into the favored regions was 98%.The predicted 3D model further characterized and analyzed using other techniques.