Internet Resources For Structural Bioinformatics

结构生物信息学的互联网资源

• 批准号: 6988453
• 负责人: STEPHEN H. BRYANT
• 金额: --
• 依托单位: NATIONAL LIBRARY OF MEDICINE
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/6988453
• 关键词: Internet; bioinformatics; chemical models; computer assisted sequence analysis; computer human interaction; computer program /software; computer simulation; computer system design /evaluation; conformation; information display; information retrieval; method development; model design /development; molecular biology information system; protein sequence; protein structure; structural biology

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.

我们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（分子建模数据库）是Entrez分子生物学检索系统的3d结构组件。MMDB是ASN.1数据库，其中描述大分子结构的所有数据项都经过验证并显式列出，因此应用程序软件不需要包含从文本格式（如PDB文件）检索这些信息所需的复杂逻辑。正在进行的管理工作增加了MMDB中大分子结构的准确分类分配。正在进行的软件开发增加了新的消息和数据类型，用于向本地观看者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（“看三维”）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，并通过万维网Entrez的MIME协议发布了一个独立版本。该软件与其他公共领域查看器的不同之处在于，它支持显示来自Entrez“结构邻居”数据库的多个对齐结构，并支持同时高亮/选择多个序列和多个结构对齐。其他功能是对同源序列的实时比对，因此Entrez用户可以轻松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，该功能还支持CDD（一个保守域数据库）的管理。最新版本还在流行的计算平台上提供了大大改进的分子图形性能。截至2004年10月，CN3D已被下载超过25万份。今年在NCBI BLAST服务器上增加了一个新的“相关结构”链接，以便在可能的情况下提供易于使用的3D结构映射。这是基于Entrez/PubMed系统中与所有蛋白质结构相似的蛋白质序列的预先计算BLAST比对的持续更新的数据库。未来的发展将考虑使用更精确的基于结构的对准方法。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域数据库的域注释，并为Entrez/Pubmed检索系统中的所有蛋白质序列提供了域注释。