Internet Resources For Structural Bioinformatics

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。工作的重点是为MMDB内的大分子结构增加准确的分类分配，创建新的信息和数据类型，以便将结构-结构比对数据传输给当地观察者，以及建立一个自动的月度更新和索引系统Pubstruct。CN3D(“See in 3D”)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，并且是可通过World-Wide-Web Entrez中的MIME协议下载的独立版本。该软件与其他公共领域查看器的不同之处在于，支持显示Entrez的“结构邻居”数据库中的多个比对结构，并支持同时突出显示/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。今年的工作集中在对CN3D的改进上。该软件已经进行了修改，使用了行业标准的3D图形库OpenGL，该图形库提供了更高质量的分子图形渲染。我们还向序列显示窗口添加了核心结构比对编辑和线程工具，以支持CDD(保守域数据库)的管理。修订和简化CN3D基础数据结构的工作正在进行中，以便在图形表示方面的进一步改进，特别是描述蛋白质家族中的保守特征，可能会添加到CN3D的未来版本中。包含这些变化的新版Cn3D于2002年6月发布，截至2002年10月已有超过5万用户下载。该版本提供了复杂的比对编辑工具，并在流行的计算平台上极大地提高了分子图形性能。截至2003年10月，CN3D的下载量超过15万份。在NCBI BLAST服务器上添加了一个新的“相关结构”链接，以便尽可能提供到3D结构的简单易用的映射。

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 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 Entrez's "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 biologist's identification of important structure-function relationships within protein families. Work this year has concentrated on improvements to CN3D. The software has been modified to use an industry-standard 3D graphics library, OpenGL, which provides much better quality molecular graphics rendering. We have also added core-structure alignment editing and threading tools to the sequence display windows, to support curation of CDD (a Conserved Domain Database). Work is in progress to revise and simplify the data structures underlying CN3D, so that further improvments in graphcis presentation, specific to describing conserved features in protein families, may be added to future versions of CN3D. A new version of Cn3D incorporating these changes was released in June, 2002 and downloaded by over 50,000 users as of October, 2002. This version provides sophisticated alignment editing tools, in addition to greatly improved molecular graphics performance on popular computing platforms. As of October, 2003, over 150,000 copies of CN3D have been downloaded. A new "related structures" link has been added to NCBI BLAST servers, to provide easy-to use mapping to 3D structure whenever possible.