COMPUTER SOFTWARE FOR ANALYSIS OF PROTEIN THREE-DIMENSIONAL STRUCTURE

本项目的目标是维护和改进PKB软件 套房. PKB是一个面向对象的数据库，包含来自 蛋白质数据库 它提供了检索 基于构象和/或序列基序的子结构数据。PKB也 提供分子图形和统计分析功能， 蛋白质亚结构PKB增加了几个新功能。 一 set提取非标准共价结构的信息，如键 辅基或金属离子，或氨基酸残基， 通过这些键进行交联。这些函数在查询中很有用 关于蛋白质-辅基相互作用，并在控制 在其他查询中存在这种交互。另一组新的 函数应用晶体学对称性生成晶体列表 包装接触和相应的对称算子。 这些功能 对研究不同的水晶环境是有用的 蛋白质，以及与晶体堆积相互作用有关的研究。 其他 新功能提取和比较蛋白质序列数据，与 晶体坐标，并确定蛋白质的“核心”子结构。 这些函数在结构属性必须 与序列数据库中的条目链接。 许多PKB功能 还进行了修改，以适应S的当前版本中的语法更改 语言，其中大部分PKB编码。PKB源已生成 通过电子邮件向社区提供。这一点的重要性 项目是在提供所需的软件工具，以创建“意见”的 蛋白质数据库，解决特定的生物学问题。PKB是 几位研究人员的工作的核心， 在美国国立卫生研究院和其他地方的结构分析和预测。 PKB也 提供了一种方法来创建一个新的数据库，专门为 同源模建

The goal of this project is to maintain and improve the PKB software suite. PKB is an object-oriented data base containing structural data from the Protein Data Bank. It provides functions for retrieval of substructure data based on conformational and/or sequence motifs. PKB also provides functions for molecular-graphic and statistical analysis of protein substructures. Several new functions have been added to PKB. One set extracts information on non-standard covalent structure, such as bonds to prosthetic groups or metal ions, or amino acid residues which are cross-linked via such bonds. These functions are useful in querys concerning protein-prosthetic group interactions, and in controlling for the presence of such interactions in other querys. Another set of new functions applies crystallographic symmetry to generate lists of crystal packing contacts and corresponding symmetry operators. These functions are useful for examining the crystalline environments of different proteins, and inquerys pertaining to crystal packing interactions. Other new functions extract and compare protein sequence data, as distinct from crystallographic coordinates, and identify protein "core" substructures. These functions are useful in retrievals where structural attributes must be linked with entries insequence data banks. Many PKB functions were also modified to accommodate syntax changes in current versions of the S language, in which much of PKB is coded. PKB source has been made available to the community via electronic mail. The importance of this project is in providing software tools needed to create "views" of the Protein Data Bank that address specific biological questions. PKB is central to the work of several researchers addressing questions instructure analysis and prediction, at NIH and elsewhere. PKB also provides a means to create a new data base designed specifically for homology modeling.