Internet Resources For Structural Bioinformatics

结构生物信息学的互联网资源

• 批准号: 6843566
• 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/6843566
• 关键词: Internet; chemical models; computer assisted sequence analysis; computer human interaction; computer program /software; computer simulation; computer system design /evaluation; conformation; informatics; information retrieval; model design /development; molecular biology information system; molecular dynamics; physical model; 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. 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.

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。工作集中在为MMDB中的大分子结构添加准确的分类法分配，创建新的消息和数据类型，以便向本地查看者传输结构结构比对数据，以及构建自动每月更新和索引系统Pubstruct。CN3D（“看三维”）是一个多结构的可视化程序，作为Entrez客户端软件的一部分分发，并且可以通过万维网Entrez的MIME协议在一个独立版本中启动。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。今年增加的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。这些软件功能旨在促进分子生物学家在蛋白质家族中重要结构-功能关系的鉴定。今年的工作主要集中在CN3D的改进上。该软件已被修改为使用行业标准的3D图形库OpenGL，它提供了更高质量的分子图形渲染。我们还在序列显示窗口中添加了核心结构对齐编辑和线程工具，以支持CDD（一个保守域数据库）的管理。修改和简化CN3D基础数据结构的工作正在进行中，以便进一步改进图形表示，特别是描述蛋白质家族的保守特征，可能会添加到CN3D的未来版本中。包含这些变化的Cn3D新版本于2002年6月发布，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校准编辑工具，除了在流行的计算平台上大大提高分子图形性能之外。截至2003年10月，CN3D已被下载超过15万份。一个新的“相关结构”链接已添加到NCBI BLAST服务器，以提供易于使用的映射到3D结构，只要可能。