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人员。MMDB（Molecular Modeling DataBase）是分子生物学检索系统的三维结构组件。MMDB是一个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PDB文件等文本格式检索此信息所需的复杂逻辑。工作集中在MMDB中添加大分子结构的准确分类分配，创建新的消息和数据类型，用于将结构-结构比对数据传输给当地观众，以及构建自动每月更新和索引系统Pubstruct。CN 3D（英语：CN 3D）是一个多结构可视化程序，作为一部分分发到Warez客户端软件中，并通过万维网Warez中的MIME协议以独立版本发布。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Zeroz的“结构邻居”数据库的多个对齐结构，以及支持同时突出显示/拾取多个序列和多个结构对齐。今年增加的其他功能是同源物序列的实时比对，这样，一个Zeroz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。这些软件功能旨在帮助分子生物学家识别蛋白质家族中重要的结构-功能关系。今年的工作重点是改进CN 3D。该软件已被修改为使用行业标准的3D图形库OpenGL，它提供了更好的质量分子图形渲染。我们还在序列显示窗口中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。工作正在进行中，以修订和简化CN 3D的数据结构，使进一步改善graphcis介绍，具体到描述蛋白质家族中的保守功能，可能会被添加到未来版本的CN 3D。2002年6月发布了包含这些更改的Cn 3D新版本，截至2002年10月，已有超过50，000名用户下载。这个版本提供了复杂的比对编辑工具，除了在流行的计算平台上大大提高分子图形性能。截至2003年10月，CN 3D的下载量已超过15万份。一个新的“相关结构”链接已被添加到NCBI BLAST服务器，以提供易于使用的映射到3D结构，只要可能。

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.