INTERNET RESOURCES FOR MOLECULAR 3D STRUCTURE

分子 3D 结构的互联网资源

• 批准号: 6111065
• 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/6111065
• 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 this year 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.

我们开发了数据库和软件， 用于蛋白质三维结构的比较分析。 这些工具免费分发给生物学家和 生物技术软件MMDB（分子建模数据库）是 分子生物学的三维结构部分 检索系统MDB是一个ASN.1数据库，其中所有数据项 描述大分子结构的方法得到验证， 列出，以便应用软件不需要包含复杂的 从文本格式检索此信息所需的逻辑， PDB文件。今年的工作重点是增加准确的 大分子结构的分类分配 内存数据库，创建新的消息和数据类型进行传输 结构-结构对齐数据的本地观众， 建立每月自动更新和索引编制系统， Pubstruct。CN 3D（“看三维”）是一种多结构 可视化程序，作为一部分分发到XNUMX客户端 软件和可通过MIME启动的独立版本 协议在万维网上的应用。该软件不同于 其他公共领域的观众在支持显示多个 来自Zeroz的“结构邻居”数据库的对齐结构， 在支持同时突出显示/拾取多个 序列和多结构比对。添加的其他功能 今年是同源序列的动态比对，所以 一个ZeroZ用户可以很容易地映射保守的序列特征， 已知的3D结构。这些软件功能旨在 以便于分子生物学家识别重要的 蛋白质家族中的结构-功能关系。