Schlessinger Avner, Ofran Yanay, Yachdav Guy, Rost Burkhard
CUBIC, Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 St Nicholas Avenue, room 804, New York, NY 10032, USA.
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D777-80. doi: 10.1093/nar/gkj053.
Immunoglobulin molecules specifically recognize particular areas on the surface of proteins. These areas are commonly dubbed B-cell epitopes. The identification of epitopes in proteins is important both for the design of experiments and vaccines. Additionally, the interactions between epitopes and antibodies have often served as a model for protein-protein interactions. One of the main obstacles in creating a database of antigen-antibody interactions is the difficulty in distinguishing between antigenic and non-antigenic interactions. Antigenic interactions involve specific recognition sites on the antibody's surface, while non-antigenic interactions are between a protein and any other site on the antibody. To solve this problem, we performed a comparative analysis of all protein-antibody complexes for which structures have been experimentally determined. Additionally, we developed a semi-automated tool that identified the antigenic interactions within the known antigen-antibody complex structures. We compiled those interactions into Epitome, a database of structure-inferred antigenic residues in proteins. Epitome consists of all known antigen/antibody complex structures, a detailed description of the residues that are involved in the interactions, and their sequence/structure environments. Interactions can be visualized using an interface to Jmol. The database is available at http://www.rostlab.org/services/epitome/.
免疫球蛋白分子能特异性识别蛋白质表面的特定区域。这些区域通常被称为B细胞表位。蛋白质中表位的鉴定对于实验设计和疫苗设计都很重要。此外，表位与抗体之间的相互作用常常被用作蛋白质-蛋白质相互作用的模型。创建抗原-抗体相互作用数据库的主要障碍之一是难以区分抗原性相互作用和非抗原性相互作用。抗原性相互作用涉及抗体表面的特异性识别位点，而非抗原性相互作用则是蛋白质与抗体上的任何其他位点之间的相互作用。为了解决这个问题，我们对所有已通过实验确定结构的蛋白质-抗体复合物进行了比较分析。此外，我们开发了一种半自动工具，用于识别已知抗原-抗体复合物结构中的抗原性相互作用。我们将这些相互作用整理成Epitome，这是一个蛋白质中结构推断抗原残基的数据库。Epitome由所有已知的抗原/抗体复合物结构、对参与相互作用的残基的详细描述及其序列/结构环境组成。可以使用Jmol界面可视化相互作用。该数据库可在http://www.rostlab.org/services/epitome/获取。
