Antigen-antibody interaction databases | Immunology system data analysis
Antibodies (Abs) are an important class of molecules used in research and increasingly as therapeutic agents to treat human diseases. Therapeutic antibodies have certain advantages over small molecules or other protein therapeutics, such as longer serum half‐lives, higher avidity and selectivity, and the ability to invoke desired immune responses. Antibody paratopes—the parts of antibodies that interact with the target antigen—can recognize almost any biomolecular target, with a large range of specificities and affinities. Knowledge of the structure of an antibody–antigen or antibody–receptor complex provides insight into how the antibody recognizes its binding partner and can guide the process of antibody design. To increase the amount of relevant binding data available for computational method validation some databases of antibody–antigen, antibody–effector, and antibody‐like protein complexes with known structures has been developped. A database enables computational benchmarking studies of existing methods and can thereby be used to drive improvements in modeling methodology.
A derived knowledge base, archives molecular interactions of protein and peptide antigens characterized by co-crystal structures. The interactions are compiled at two levels, viz. residue level and atomic level. The interactions are characterized using AAIF (Antigen-Antibody Interaction Finder) developed in-house. AAIF enlists various non-covalent interactions such as van der Waals, salt bridges, hydrogen bonds and short contacts using distance and geometry-based criteria.
Reports a diverse set of antibody binding data with accompanying structures that can be used to evaluate methods for modeling antibody interactions. AB-Bind includes 1101 mutants with experimentally determined changes in binding free energies across 32 complexes. The database entries were manually curated and organized. It focuses on antibody binding affinity measurements with significant contribution of non-Ala mutations.