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

蛋白质数据库(PDB)包含大分子的原子结构。截至1991年10月，有790个结构条目(196兆字节)，如果目前的增长速度保持下去，这个数字到本十年末可能增长到10000个。这些数据为理解生物功能提供了机会，例如，通过比较结构研究。这项工作解决了几个挑战，首先是使PDB更容易为分子生物学家和结晶学家所用，其次是帮助管理越来越多的数据。几个软件开发是并行进行的，但共享相同的类库。首先，一种新的基于对象的PDB存储格式提供了对在大分子中发现的亚结构水平的适当访问。第二，基于对象的软件工具正在从现有的结构化程序中派生出来，这些工具可以询问和处理结构数据，并帮助结构验证。最后，高级查询语言提供了与PDB的直观和直接交互。软件开发的每个方面都是通过原型化进行的，然后是在实验室中反复测试和代码修改。这项工作集成了面向对象数据库和知识库等数据库研究成果，组件等软件工程成果和扩展事务模型等粘合协同工作，以支持协同科研。通过允许以更直观的方式进行数据查询，这些工具可能会潜在地加速发现新的结构-功能关系。

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.