Comparative Homology Modelling for HPV Type 16 E 7 Proteins by using MODELLER and its Validations with SAVS and ProSA Web Server

Abstract

Human papillomaviruses (HPV) are a group of viruses which are associated with various proliferative diseases in the infected epithelium. HPV types 6, 11, 16, and 18 are the most common, are associated with lesions in the anogenital tract. The benign types 6 and 11 are mainly associated with condylomata acuminate of the oncogenic HPV types, HPV-16 is most frequently found in cervical carcinomas. The 3-dimentional structure of the protein was not yet available in Protein Data Bank; hence the present paper of predicting the 3D model of the HPV Type 16 E7 proteins. Template based homology modelling predicts the three-dimensional structure of hpv type 16 E 7 protein sequence (target) based primarily on its alignment to one or more proteins of known structure as template generated by MODELLER. The prediction process consists of target-template alignment, model building, and model evaluation. The model was checked for stereo chemical quality by PROCHECK, VERIFY 3D, WHAT IF, ERRAT AND ProSA servers were also used for the display of Z-scores and energy plots. Finally the protein was visualized with Swiss-PDB viewer.