INTERNET RESOURCES FOR MOLECULAR 3D STRUCTURE

分子 3D 结构的互联网资源

• 批准号: 6162797
• 负责人: S 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/6162797
• 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. These software systems fall in three categories, PKB, a database for computational biology researchers, MMDB, a database for multi-platform software developers, and CN3D, an end-user 3D visualization tool for the molecular information browser Entrez. PKB is an object oriented system based on the S language. In the past year PKB has been extended by addition of protein threading routines, and is for this reason now in use in many research laboratories. New structure validation routines have also been added to PKB, and it is for this reason now used routinely at the Protein Data Bank, to identify and correct errors in newly-deposited 3D data files. 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 PDB files. Work this year has concentrated on MMDB-API (applications programming interface to MMDB), the in-memory representation of 3D structure information as a C data structure. Useful derived data have also been added, including uniformly defined secondary structure and domain boundary annotation, and complete cross references to NCBI sequence databases and Medline. The MMDB is now distributed as the "structure" database in Entrez, and its API as part of the NCBI toolkit. CN3D (`see in three dimensions'), written this year, 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 the Entrez "structure neighbors" database, and in supporting simultaneous highlighting/picking of multiple sequence and multiple structure alignments. These features are intended to facilitate molecular biologist's identification of important structure-function relationships within protein families.

我们已经开发了数据库和软件，用于 蛋白质三维结构的比较分析 结构。这些工具免费分发给生物学家 以及生物技术软件的开发者。这些软件 系统分为三类，PKB，一个用于 计算生物学研究人员，MMDB，一个数据库 多平台软件开发人员，以及最终用户CN3D 用于分子信息浏览器的三维可视化工具 请进。PKB是在S的基础上开发的面向对象系统 语言。在过去的一年里，PKB被延长了 添加蛋白质线程例程，并用于此 现在许多研究实验室都在使用这一理由。新的 结构验证例程也已添加到PKB， 正是出于这个原因，它现在被常规用于蛋白质 数据库，用于识别和纠正中的错误 新存放的3D数据文件。MMDB是ASN.1数据库 其中描述大分子结构的所有数据项 都经过验证并明确列出，因此应用程序 软件不需要包含所需的复杂逻辑 从PDB文件中检索此信息。今年的工作 专注于MMDB-API(应用程序编程 与MMDB的接口)，3D的内存表示 将信息结构化为C数据结构。有用的派生 还添加了数据，包括统一定义的数据 二级结构和区域边界注释，以及 对NCBI序列数据库的完整交叉引用和 梅德莱恩。MMDB现在以“结构”的形式分发 Entrez中的数据库及其作为NCBI一部分的API 工具包。CN3D(‘See in 3D’)，编写如下 年，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，并在 中可通过MIME协议提供的独立版本 万维网Entrez。该软件与其他软件不同 支持多个显示的公共域观看者 对齐的结构，来自Entrez的“结构邻居” 数据库，并在支持同步 高亮显示/拾取多个序列和多个 结构路线。这些功能旨在 便于分子生物学家鉴定 蛋白质中重要的结构-功能关系 家人。