INTERNET RESOURCES FOR MOLECULAR 3D STRUCTURE

我们已经开发了用于蛋白质三维结构比较分析的数据库和软件。这些工具免费分发给生物学家和生物技术软件开发商。MMDB(分子建模数据库)是Entrez分子生物学检索系统的三维结构组件。MMDB是ASN.1数据库，其中所有描述大分子结构的数据项都经过验证并明确列出，因此应用软件不需要包含从文本格式(如PDB文件)检索该信息所需的复杂逻辑。今年的工作集中在为MMDB内的大分子结构增加准确的分类分配，创建用于向当地观众传输结构-结构比对数据的新的消息和数据类型，以及构建一个自动的每月更新和索引系统Pubstruct。CN3D(见三维)是一个多结构可视化程序，作为Entrez客户端软件的一部分分发，并且是一个独立版本，可通过World-Wide-Web Entrez中的MIME协议下载。该软件与其他公共领域查看器的不同之处在于，支持显示来自Entrezs结构邻居数据库的多个比对结构，并支持同时突出/挑选多个序列和多个结构比对。今年增加的其他功能是同源物序列的即时比对，因此Entrez用户可以很容易地将保守的序列特征映射到已知的3D结构上。这些软件功能旨在促进分子生物学家识别蛋白质家族中重要的结构-功能关系。-大分子三维结构数据库分子建模-既不是人体受试者也不是人体组织

We have developed databases and software useful for comparative analysis of protein three-dimensional structure. These tools are distributed freely to biologists and developers of biotechnology software. MMDB (Molecular Modeling DataBase) is the 3D-structure component of the Entrez molecular biology retrieval system. MMDB is an ASN.1 database where all data items describing macromolecular structure are validated and explicitly listed, so that application software need not contain the complex logic required to retrieve this information from text formats such as PDB files. Work this year has concentrated on addition of accurate taxonomy assignments for macromolecular structures within MMDB, creation of new message and data types for transmission of structure-structure alignment data to local viewers, and on construction of an automated monthly update and indexing system, Pubstruct. CN3D (see in three dimensions) is a multi-structure visualization program distributed as part to the Entrez client software and in a stand-alone version lauchable via the MIME protocol in World- Wide-Web Entrez. The software differs from other public domain viewers in supporting display of multiple aligned structures from Entrezs structure neighbor database, and in supporting simultaneous highlighting/picking of multiple sequence and multiple structure alignments. Other features added this year are on-the-fly alignment of the sequences of homologs, so that an Entrez user may easily map conserved sequence features onto the know 3D structure. These software features are intended to facilitate molecular biologists identification of important structure-function relationships within protein families. - macromolecular 3D structure database molecular modeling - Neither Human Subjects nor Human Tissues