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。正在进行的策展工作为MMDB中的大分子结构增加了准确的分类分配。正在进行的软件开发增加了新的信息和数据类型，用于向当地观众传输结构-结构对齐数据，以及高度自动化的每月更新和索引系统Pubstruct。Cn 3D（英语：Cn 3D）是一个多结构的可视化程序，它作为Cn 3D客户端软件的一部分分发，并通过万维网Cn 3D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。其他功能是同源物序列的即时比对，因此，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。为了方便分子生物学家识别蛋白质家族中重要的结构-功能关系，我们在Cn 3D的序列显示窗口中添加了核心结构比对编辑和线程工具，该功能还支持CDD（保守结构域数据库）的管理。最新版本还在流行的计算平台上提供了大大改进的分子图形性能。截至2004年10月，CN 3D的下载量已超过25万份。一个新的“相关结构”链接已被添加到NCBI BLAST服务器今年，以提供易于使用的映射到3D结构，只要可能。这是基于一个不断更新的数据库的预先计算的BLAST比对的蛋白质序列在Zeroz/PubMed系统与所有的蛋白质结构，他们是相似的。未来的发展将考虑更精确的基于结构的比对方法的用户。今年还开发了一个完全重新设计的保守领域架构研究工具（CDART）数据库。它为MMDB蛋白质结构显示提供了来自保守结构域数据库的结构域注释，并为所有蛋白质序列提供了结构域注释。

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. Ongoing curatorial work has added of accurate taxonomy assignments for macromolecular structures within MMDB. Ongoing software development has added new message and data types for transmission of structure-structure alignment data to local viewers, and a highly 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 launched 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 are on-the-fly alignment of the sequences of homologs, so that an Entrez user may easily map conserved sequence features onto the known 3D structure. To facilitate molecular biologist's identification of important structure-function relationships within protein families we have added core-structure alignment editing and threading tools to Cn3D's sequence display windows, a feature which also supports curation of CDD (a Conserved Domain Database). The latest version also provides greatly improved molecular graphics performance on popular computing platforms. As of October, 2004, over 250,000 copies of CN3D have been downloaded. A new "related structures" link has been added to NCBI BLAST servers this year, to provide easy-to use mapping to 3D structure whenever possible. This is based on a continuously updated database of pre-computed BLAST alignments of protein sequences in the Entrez/PubMed system with all protein structures to which they are similar. Future development will consider user of more accurate structure-based alignment methods. A completely re-engineered version of the Conserved Domain Architecture Research Tool (CDART) database has also been developed this year. It provides domain annotations derived from the Conserved Domain Database for MMDB protein structure displays as well as domain annotation for all protein sequences in the Entrez/Pubmed retrieval system.