EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB).
EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB).
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DOI：
10.1186/1745-7580-3-3
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发表时间：
2007-02-21
期刊：
影响因子：
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通讯作者：
Ponomarenko JV
中科院分区：
文献类型：
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作者：
Beaver JE;Bourne PE;Ponomarenko JV
表位的结构信息，特别是抗原与免疫受体复合物的三维（3D）结构，为免疫学提供了宝贵的数据来源。这些信息可在蛋白质数据库（PDB）中获得，并由免疫表位数据库和分析资源（IEDB）以策划形式提供。随着这些数据的持续增长和理解免疫学兴趣分子水平相互作用的重要性，需要新的专门的分子可视化和分析工具。EpitopeViewer是一个独立于平台的Java应用程序，用于可视化表位的三维结构和序列，并分析它们与免疫系统抗原特异性受体（抗体、T细胞受体和MHC分子）的相互作用。通过读取来自IEDB的整理数据和/或从PDB的原子坐标实时计算，查看器可以呈现抗原和受体之间分子间相互作用的3D视图和二维图。可以保存3D视图和相关交互以供将来使用和发布。EpitopeViewer可以从IEDB网站通过快速链接“按3D结构浏览记录”访问。该EpitopeViewer的设计和测试使用的免疫学家在分子图形很少或没有培训。EpitopeViewer可以从大多数流行的Web浏览器启动，无需用户干预。要求Java Runtime Environment (RJE) 1.4.2及以上版本。
Structural information about epitopes, particularly the three-dimensional (3D) structures of antigens in complex with immune receptors, presents a valuable source of data for immunology. This information is available in the Protein Data Bank (PDB) and provided in curated form by the Immune Epitope Database and Analysis Resource (IEDB). With continued growth in these data and the importance in understanding molecular level interactions of immunological interest there is a need for new specialized molecular visualization and analysis tools. The EpitopeViewer is a platform-independent Java application for the visualization of the three-dimensional structure and sequence of epitopes and analyses of their interactions with antigen-specific receptors of the immune system (antibodies, T cell receptors and MHC molecules). The viewer renders both 3D views and two-dimensional plots of intermolecular interactions between the antigen and receptor(s) by reading curated data from the IEDB and/or calculated on-the-fly from atom coordinates from the PDB. The 3D views and associated interactions can be saved for future use and publication. The EpitopeViewer can be accessed from the IEDB Web site through the quick link 'Browse Records by 3D Structure.' The EpitopeViewer is designed and been tested for use by immunologists with little or no training in molecular graphics. The EpitopeViewer can be launched from most popular Web browsers without user intervention. A Java Runtime Environment (RJE) 1.4.2 or higher is required.