DATABASES FOR MOLECULAR MODELING

我们开发了数据库和软件， 蛋白质三维比较分析 结构这些工具免费分发给生物学家 和生物技术软件的开发者。这些软件 系统分为三类，PKB，用于 计算生物学研究人员，MMDB，一个数据库， 多平台软件开发商和最终用户CN 3D 分子信息浏览器的3D可视化工具 你好 PKB是一个基于S 语言在过去的一年里，PKB已经延长了 添加蛋白质线程例程，并为此 目前，许多研究实验室都在使用。新 结构化验证程序也被添加到PKB中， 正因如此，现在蛋白质 数据库，以确定和纠正错误， 新存放的3D数据文件。MDB是一个ASN.1数据库 其中描述大分子结构的所有数据项 经过验证并明确列出，以便应用程序 软件不需要包含复杂的逻辑， 从PDB文件中检索此信息。今年工作 专注于MMDB-API（应用程序编程 MMDB的接口），3D的内存表示 结构化信息作为C数据结构。有用的派生 还增加了数据，包括统一定义的 二级结构和结构域边界注释，以及 完整的交叉引用NCBI序列数据库， Medline. MMDB现在作为“结构”分发 数据库及其作为NCBI一部分的API 工具箱。 CN 3D（“看到三维”），这样写的 年，是一个多结构可视化程序 作为一部分分发到Zeroz客户端软件，并在 一个独立的版本，可通过MIME协议启动， 万维网网址该软件不同于其他 公共领域的观众在支持显示多个 排列的结构，从“结构邻居” 数据库，并支持同时 多个序列和多个 结构调整。这些功能旨在 便于分子生物学家鉴定 蛋白质中重要结构-功能关系 家庭

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.