Generation of Structural Homology Models

To determine the conserved regions, homology models were generated for the translated F and HN proteins by aligning sequences for each gene separately using multiple sequence alignment (MSA) with the aid of ClustalW as implemented in the Bioedit program version 7.0 (38) and or Jalview. The consensus regions for each protein in each group (poultry, waterfowl, and vaccine) were used in a BLAST search against the protein Data Bank (PDB), to identify the available homologs or orthologous of known proteins. Structural homology modeling was also done using tools of SWISS-MODEL modeling server and viewed by deep viewer v4.01 (40). Overall, PDB entries 3MAW and 3T1E were used as templates for the F protein and HN protein, respectively. The experimental 3D structure (3MAW) of F protein from ND virus had identity and similarity scores of LaSota (71.1 and 74.3%), waterfowl (71.6 and 74.3%), and poultry (72.3 and 74.5%), respectively. Selected templates were subjected to chimeras to replace amino acids with Avulavirus F and HN protein consensus sequence. Energy minimization was carried out with YASARA force field in YASARA version 18.4.24, to obtain the most stable local minimum protein conformation. Later on, correctness of models was established using PROSTAT (module in homology) and PROCHECK (41), and the candidate epitopes were analyzed by different predication tools for structurally conserved regions (SCRs), loops, and accuracy.