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。正在进行的策展工作增加了对MMDB内大分子结构的准确分类指定。正在进行的软件开发增加了新的消息和数据类型，用于向当地观众传输结构-结构对齐数据，以及一个高度自动化的每月更新和索引系统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，并且是通过万维网Entrez中的MIME协议启动的独立版本。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。其他特征是同源序列的即时比对，因此Entrez用户可以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Cn3D的序列显示窗口中添加了核心结构比对编辑和线程工具，这一功能也支持CDD(保守域数据库)的管理。最新版本还在流行的计算平台上提供了极大改进的分子图形性能。今年，NCBI BLAST服务器增加了一个新的“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。这是基于Entrez/PubMed系统中所有与蛋白质结构相似的蛋白质序列的预计算BLAST比对的不断更新的数据库。未来的发展将考虑用户使用更精确的基于结构的配准方法。今年还开发了一个完全重新设计的保守领域体系结构研究工具(CDART)数据库版本。它为MMDB蛋白质结构显示提供从保守域数据库派生的域注释，以及Entrez/Pubmed检索系统中所有蛋白质序列的域注释。截至2005年9月，Cn3D的下载量已超过30万份。Entrez的结构数据库资源平均每天由30,000名用户使用，平均每小时约有4000次网络点击。

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. 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. As of September, 2005, over 300,000 copies of Cn3D have been downloaded. Entrez's structure database resources are used by an average of 30,000 users per day, at rates averaging about 4000 web hits per hour.