AgAbDb

Antigen-Antibody Interaction Database (AgAbDb) is an immunoinformatics resource developed at the Bioinformatics Centre, University of Pune, and is available online at http://bioinfo.net.in/AgAbDb.htm. Antigen-antibody interactions are a special class of protein-protein interactions that are characterized by high affinity and strict specificity of antibodies towards their antigens. Several co-crystal structures of antigen-antibody complexes have been solved and are available in the Protein Data Bank (PDB). AgAbDb is a derived knowledgebase developed with an objective to compile, curate, and analyze determinants of interactions between the respective antigen-antibody molecules. AgAbDb lists not only the residues of binding sites of antigens and antibodies, but also interacting residue pairs. It also helps in the identification of interacting residues and buried residues that constitute antibody-binding sites of protein and peptide antigens. The Antigen-Antibody Interaction Finder (AAIF), a program developed in-house, is used to compile the molecular interactions, viz. van der Waals interactions, salt bridges, and hydrogen bonds. A module for curating water-mediated interactions has also been developed. In addition, various residue-level features, viz. accessible surface area, data on epitope segment, and secondary structural state of binding site residues, are also compiled. Apart from the PDB numbering, Wu-Kabat numbering and explicit definitions of complementarity-determining regions are provided for residues of antibodies. The molecular interactions can be visualized using the program Jmol. AgAbDb can be used as a benchmark dataset to validate algorithms for prediction of B-cell epitopes. It can as well be used to improve accuracy of existing algorithms and to design new algorithms. AgAbDb can also be used to design mimotopes representing antigens as well as aid in designing processes leading to humanization of antibodies.

抗原-抗体相互作用数据库（AgAbDb）是由普纳大学生物信息学中心开发的免疫信息学资源，可通过http://bioinfo.net.in/AgAbDb.htm在线访问。抗原-抗体相互作用属于一类特殊的蛋白质-蛋白质相互作用，其特征为抗体对抗原具有高亲和力与严格的特异性。目前已有多套抗原-抗体复合物的共晶体结构被解析，并可通过蛋白质数据银行（Protein Data Bank，PDB）获取。

AgAbDb是一类衍生知识库，其开发宗旨为收集、整理并分析抗原-抗体分子间相互作用的决定因素。该数据库不仅收录了抗原与抗体结合位点的残基信息，还包含相互作用残基对的数据，同时可辅助识别构成蛋白质与肽类抗原抗体结合位点的相互作用残基与埋藏残基。

自研程序抗原-抗体相互作用检索工具（Antigen-Antibody Interaction Finder，简称AAIF）用于收集分子间相互作用，即范德华相互作用、盐桥与氢键。同时团队还开发了用于处理水介导相互作用的注释模块。此外，该数据库还收集了多种残基水平的特征信息，包括可及表面积、表位片段数据以及结合位点残基的二级结构状态。

除采用PDB编号外，该数据库还为抗体残基提供了吴-卡巴特编号（Wu-Kabat numbering）以及互补决定区（complementarity-determining regions）的明确定义。用户可通过Jmol程序可视化展示分子间相互作用。

AgAbDb可作为基准数据集，用于验证B细胞表位预测算法的性能；同时也可用于提升现有算法的预测精度，并助力新型算法的开发。此外，该数据库还可用于设计模拟抗原的模拟表位，同时辅助开发抗体人源化相关工艺。