DATABASES FOR MOLECULAR MODELING

我们已经开发了对蛋白质建模有用的数据库和软件 三维结构与层序结构分析 两性关系。这些工具已经免费分发给生物学家 以及生物技术软件的开发者。这项工作可分为 三个方面：1)继续发展面向对象的“PKB” 研究数据库，2)制作描述蛋白质的GenBank条目 和已知结构的核酸，以及3)设计和实现 为分子建模开发人员提供方便的结构数据库 软件。PKB数据规范已扩展到包括所有 蛋白质数据库定义的数据项，包括科学 文献引用和联系。我们还添加了 恢复生物聚合物正确定义的验证程序 序列和化学修饰，并识别立体化学 反常现象。我们已使用PKB生成ASN.1语言的报告 结构特征可映射到序列，使用当前的NCBI/GenBank 数据规范。这些数据已更新为新结构 可从蛋白质数据库获得，并被合并到 广泛分布的GenBank/ASN.1和Entrez数据库。要提供 从现代应用程序方便地访问结构数据 我们已经开始开发一个用C编写的ASN.1数据库，其中包含 完整的共价和空间结构数据。它的规格允许 生物大分子与非生物大分子组成的比较 根据大分子的化学结构，并直接 通过对齐推断的三维结构的表示 同源的或化学上相似的分子。这件事的意义 工作是为生物学家提供轻松访问结构数据的途径，以及 为有兴趣的研究人员提供软件基础设施 序列-结构关系和开发分子的程序设计 建模软件。

We have developed databases and software useful for modeling of protein three-dimensional structure and analysis of sequence-structure relationships. These tools have been distributed freely to biologists and developers of biotechnology software. The work may be divided into three areas: 1) continued development of the "PKB" object-oriented research database, 2) production of GenBank entries describing proteins and nucleic acids with known structure, and 3) design and implementation of a structural database convenient for developers of molecular modeling software. The PKB data specification has been expanded to include all data items defined by the Protein Data Bank, including scientific literature citations and bonded connectivity. We have also added validation procedures which recover correct definitions of biopolymer sequence and chemical modification, and identify stereochemical anomalies. We have used PKB to produce ASN.1-language reports of structural features mapable to sequence, using the current NCBI/GenBank data specification. These data have been updated as new structures became available from the Protein Data Bank, and incorporated into the widely distributed GenBank/ASN.1 and Entrez databases. To provide convenient access to structural data from modern application programs written in C we have begun development of an ASN.1 database containing complete covalent and spatial structure data. Its specification allows comparison of biopolymer or non-biopolymer components of biological macromolecules according to chemical structure, and direct representation of three-dimensional structure inferred by alignment with homologous or chemically similar molecules. The significance of this work is in providing biologists with easy access to structural data, and in providing a software infrastructure to researchers interested in sequence-structure relationships and programmers developing molecular modeling software.