An Object-Oriented Toolbox for Use with the Protein Data Bank (PDB)

蛋白质数据库（PDB）包含以下原子结构： 大分子截至1991年10月，共有790个建筑物。 条目（196兆字节），如果目前的增长率持续下去， 到本十年结束时，这一数字可能会增加到10 000。数据 提供了解生物功能的机会 通过比较结构研究。 这项工作 解决了首先使PDB更 分子生物学家和晶体学家都可以访问， 特别是，第二，协助管理日益增加的 大量的数据。一些软件开发正在进行中。 并行进行，但共享相同的类库。 首先，一种新的基于对象的PDB存储格式提供了合适的 进入大分子中发现的亚结构水平。 第二，基于对象的软件工具， 操作结构数据，并协助结构验证 都是从现有的结构化程序中派生出来的。最后 高级查询语言提供了直观和直接 与PDB的互动。软件开发的各个方面 通过原型设计，然后是迭代的测试循环来进行 在实验室和代码修改。这项工作整合了 最先进的数据库研究成果，如面向对象 数据库和知识库，软件工程成果， 作为组件和胶水协作工作， 支持合作科学研究的交易模式。 这些工具可能会加速发现新的 结构-功能关系，允许在 更直观的时尚。

The Protein Data Bank (PDB) contains the atomic structure of macromolecules. As of October 1991 there were 790 structural entries (196 Mbytes), if current growth rates persist, this number could grow to 10,000 by the end of the decade. The data provide opportunities for understanding biological function through, for example, comparative structural research. This work addresses several challenges in first making the PDB more accessible to molecular biologists and crystallographers in particular, and second assisting in the management of increasing amounts of data. Several software developments are being undertaken in parallel, but share the same class libraries. First, a new object-based PDB storage format provides suitable access to the levels of substructure found in macromolecules. Second, object-based software tools that interrogate and manipulate structural data, and assist in structure verification are being derived from existing structured programs. Finally, a high-level query language provides intuitive and direct interaction with the PDB. Each aspect of software development proceeds by prototyping followed by iterative cycles of testing in the laboratory and code modification. This work integrates the state-of-art database research results such as object-oriented databases and knowledge bases, software engineering results such as component and glue collaborative work such as extended transaction models to support cooperative scientific research. These tools could potentially precipitate the discovery of new structure-function relationships by permitting data query in a more intuitive fashion.