INTERNET RESOURCES FOR MOLECULAR 3D STRUCTURE

分子 3D 结构的互联网资源

• 批准号: 6432750
• 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/6432750
• 关键词: Internet; chemical information system; chemical models; computer assisted sequence analysis; computer human interaction; computer program /software; computer simulation; computer system design /evaluation; conformation; information retrieval; model design /development; physical model; protein sequence; protein structure

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, Open GL, 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.

我们开发了可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 是一个 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明确列出，因此应用程序软件不需要包含从 PDB 文件等文本格式检索此信息所需的复杂逻辑。工作重点是为 MMDB 中的大分子结构添加准确的分类分配，创建新的消息和数据类型以将结构-结构比对数据传输给本地查看器，以及构建每月自动更新和索引系统 Pubstruct。 CN3D（“三维可视化”）是一种多结构可视化程序，作为 Entrez 客户端软件的一部分分发，并以独立版本通过万维网 Entrez 中的 MIME 协议进行发布。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 Entrez 的“结构邻居”数据库的多个比对结构，并支持同时突出显示/选取多个序列和多个结构比对。今年添加的其他功能包括同源序列的动态比对，以便 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识别蛋白质家族内重要的结构-功能关系。今年的工作重点是 CN3D 的改进。该软件经过修改，可以使用行业标准的 3D 图形库 Open GL，它可以提供质量更高的分子图形渲染。我们还在序列显示窗口中添加了核心结构比对编辑和线程工具，以支持 CDD（保守域数据库）的管理。修订和简化 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中的保守特征，可能会添加到 CN3D 的未来版本中。