Biological databases useful for epitope mapping and immune response simulation

The application of bioinformatics has facilitated the development of subareas of science and subspecialties, such as immunoinformatics. Immunoinformatics is extremely useful in vaccine development, the prediction of potential epitopes, and the simulation of immune responses. However, this requires the availability of curated, high-quality data that has been experimentally tested and validated. This study describes databases that are useful in epitope mapping and immune response simulation. The Immune Epitope Database and Analysis Resource, Universal Protein Resource, and Protein Data Bank are three such databases that are relevant for the use of immunoinformatics tools in epitope mapping and immune response simulation. These databases, together with others, whether general or specialized, form part of the biological data ecosystem on which most immunoinformatics tools for epitope prediction and immune response simulation are built and operate. All have their advantages and limitations, so the selection of one or the other should be based on an analysis of the needs and objectives of the researcher and their projects.