Antibody Engineering for Pursuing a Healthier Future

Saeed, Abdullah F. U. H.; Wang, Rongzhi; Ling, Sumei; Wang, Shihua

Computational and bioinformatics approaches play an essential role for antibody selection and epitope prediction. It is an interdisciplinary science and the term can be defined as "the application of computer tools to handle biological information." Several computational and bioinformatics tools for prediction of antibody binders include RANKPEP, nHLAPred, NetMHC, kernel-based inter-allele peptide binding prediction system (KISS) with support vector machine (SVM; Bhasin and Raghava, 2007; Lundegaard et al., 2008) . Moreover, these tools use databases that contain known epitopes from SYFPEITHI, MHCBN, LANL, and IEDB for protein epitope prediction (Soria-Guerra et al., 2015) . Furthermore, other tools include position specific scoring matrices (PSSM) used for sequence alignment, IEDB analysis resource database uses NetMHCpan for peptide affinity, quantitative matrices (QM), whole antigen processing pathway (WAPP), Matthews correlation coefficient (MCC), and spatial epitope prediction of protein antigens (SEPPA) (Soria-Guerra et al., 2015) . Recently, a simulation tool C-ImmSim was developed for the study of a number of different immunological processes. The processes include simulations of immune response by representing pathogens, as well as lymphocytes receptors, amino acid sequences and T and B cell epitope prediction (Rapin et al., 2010) .