Structural Epitope Database (SEDB): A Web-based Database for the Epitope, and its Intermolecular Interaction Along with the Tertiary Structure Information

Abstract

An epitope is an antigenic determinant. It is a part of antigen, which is recognized by specific receptor of the immune system, exclusively by antibodies, B-cells or T-cells. Thus, exhaustive molecular knowledge of epitopes will have great implications for vaccine and drug design. Existing epitope databases are lacking complete structural information of epitopes. Therefore, we have developed an open-access database for describing the three-dimensional structure of epitopes and its interaction with antigens and antibodies. We have cataloged 619 epitope structures from Protein Data Bank and published research articles. Our database provides an extensive collection of B-cell, T-cell and MHC binding proteins. For user convenience, these epitopes have been classified based on structure (Linear epitope and Discontinuous epitope) and cell types (B-cell, T-cell and MHC binding). Our database incorporates specialized features of epitopes, including complex ID, epitope sequence, epitope length, epitope position, source information, structure determination method, taxonomic ID and antigen-antibody interacting residues. It also summarizes multi domain protein's structural information like protein name, polypeptide type, molecule name, chain ID, fragment length, sequence length and amino acid sequence. Additionally, it provides Gene-Ontology, MolProbity and Epitope visualization tool for better and clear understanding of the epitope conformation and its interaction with protein. The user interface is cross linked to other public databases like IEDB, UniprotKB, PDB, NCBI and other existing epitope database for making it more informative. The user friendly web page is freely available at URL http:// sedb.bicpu.edu.in.

An Introduction to B-Cell Epitope Mapping and In Silico Epitope Prediction

“…SEDB collects related information of epitopes, like gene-ontology information, Ag-Ab interaction graph, and epitopes location in protein with interaction data, which are missing in currently available epitope databases [62]. …”

Immunogenicity of Protein Pharmaceuticals

“…Due to technological advances in proteomics and sequence mapping, epitope databases have been constructed that provide a library of existing epitopes and methods of prediction. Several databases exist such as IEDB, Epitome, and SEDB [208][209][210] , that provide information on two dimensional epitopes that are recognized by T cells.…”

Proteomics in India: the clinical aspect

“…Researchers at IISc, Bangalore have developed quite a few protein databases related to structure and function of protein kinases like ‘KinG’, NrichD, PALI, PRODOC and MulPSSM [142–144]. A number of protein databases such as PepBind, Immune Epitope Prediction Database & Tools, SEDB, Clostridium-DT(DB), and VPDB have originated from the Center of Bioinformatics in Pondicherry University [145–147]. Databases of protein features, resources for signaling and metabolic pathways intrinsic to specific biological processes, and repositories of disease-specific molecular level changes will help researchers use systems biology approaches to understand disease mechanisms in greater detail.…”