Designing of CD8(+) and CD8(+)-overlapped CD4(+) epitope vaccine by targeting late and early proteins of human papillomavirus

Kaliamurthi, Satyavani; Selvaraj, Gurudeeban; Kaushik, Aman Chandra; Gu, Ke-Ren; Wei, Dong-Qing

Prediction of peptide structure and homology modeling PEP-FOLD3 was used to predict the chemical structure of the selected antigenic proteins. 51 Hidden Markov model suboptimal conformation sampling approach was applied to predict the structure from the input peptide sequence. For confirmation, 200 simulation runs were selected and the different cluster models were sorted by the sOPEP energy. 52 Phyre2 and Iterative Threading ASSEmbly Refinement (I-TASSER) were used to predict the three-dimensional (3D) structure of target receptors. The Phyre2 is a protein modeling and analysis engine which uses highly innovative remote homology detection methods to accurately construct the 3D structure of targets within a duration of 30 minutes to 2 hours. 53 I-TASSER is another vital protein structure prediction tool that identifies the respective structural templates from the Protein Data Bank (PDB) through local meta-threading server (LOMETS) with full-length atomic models created by the repetitive template fragment