title: Major histocompatibility complex linked databases and prediction tools for designing vaccines.
abstract: Presently, the major histocompatibility complex (MHC) is receiving considerable interest owing to its remarkable role in antigen presentation and vaccine design. The specific databases and prediction approaches related to MHC sequences, structures and binding/nonbinding peptides have been aggressively developed in the past two decades with their own benchmarks and standards. Before using these databases and prediction tools, it is important to analyze why and how the tools are constructed along with their strengths and limitations. The current review presents insights into web-based immunological bioinformatics resources that include searchable databases of MHC sequences, epitopes and prediction tools that are linked to MHC based vaccine design, including population coverage analysis. In T cell epitope forecasts, MHC class I binding predictions are very accurate for most of the identified MHC alleles. However, these predictions could be further improved by integrating proteasome cleavage (in conjugation with transporter associated with antigen processing (TAP) binding) prediction, as well as T cell receptor binding prediction. On the other hand, MHC class II restricted epitope predictions display relatively low accuracy compared to MHC class I. To date, pan-specific tools have been developed, which not only deliver significantly improved predictions in terms of accuracy, but also in terms of the coverage of MHC alleles and supertypes. In addition, structural modeling and simulation systems for peptide-MHC complexes enable the molecular-level investigation of immune processes. Finally, epitope prediction tools, and their assessments and guidelines, have been presented to immunologist for the design of novel vaccine and diagnostics.
authors.affiliation: Amity Institute of Biotechnology, Amity University Uttar Pradesh (Lucknow Campus), Malhaur, Gomti Nagar Extension, Lucknow 226028, India. Electronic address: spsingh5@amity.edu.
authors.forename: Satarudra Prakash
authors.initials: SP
authors.lastname: Singh
authors.affiliation: Institute of Engineering and Technology, U.P. Technical University, Lucknow 226021, India.
authors.forename: Bhartendu Nath
authors.initials: BN
authors.lastname: Mishra
mesh_terms: D000483:Alleles; D017951:Antigen Presentation; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D018604:Epitope Mapping / Q000379:methods; D018984:Epitopes, T-Lymphocyte / Q000235:genetics / Q000276:immunology; D006801:Humans; D008285:Major Histocompatibility Complex / Q000235:genetics* / Q000276:immunology*; D010455:Peptides / Q000235:genetics / Q000276:immunology; D046988:Proteasome Endopeptidase Complex / Q000378:metabolism; D011485:Protein Binding; D012984:Software; D014612:Vaccines / Q000235:genetics / Q000276:immunology*; D064878:Web Browser
chemical_list: D018984:Epitopes, T-Lymphocyte; D010455:Peptides; D014612:Vaccines; D046988:Proteasome Endopeptidase Complex
keywords: Epitope; Immunoinformatics; MHC; Prediction; Supertype; Vaccine