Papers by Upasna Srivastava
The aim of In-silico structural analysis and Protein disorder prediction for HPV type 16 E7 virus... more The aim of In-silico structural analysis and Protein disorder prediction for HPV type 16 E7 virus proteins is to solve the problem of designing vaccine against cervical cancer. The simultaneous structural analysis of E7 proteins out of 50 different HPV strains was carried out for prediction and validation, by using different bioinformatics tools such as CPH Model,TMHMM Server,DisEMBL and GlobPlot. In this CPH Model gives the template recognition, which is based on profile-profile alignment and it also create a model for HPV type 16 E7 protein sequence. The TMHMM Server gives prediction of transmembrane helices and discriminate between soluble and membrane proteins with high degree of accuracy show as graphical form. DisEMBL gives prediction of disordered/unstructured regions within a protein sequence of HPV 16 E7 protein andGlobPlot also predict theorder/globularity and disordered domain for protein sequence.
Human papillomaviruses (HPV) are a group of viruses which are associated with various proliferati... more 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.
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Papers by Upasna Srivastava