DATABASES FOR MOLECULAR MODELING

分子建模数据库

• 批准号: 5203627
• 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/5203627
• 关键词: chemical information system; chemical models; computer assisted sequence analysis; computer network; computer program /software; computer simulation; computer system design /evaluation; physical model; protein sequence; protein structure

We have developed databases and software useful for molecular modeling and analysis of sequence-structure relationships. These tools are distributed freely to biologists and developers of biotechnology software. Work has concentrated in three areas: 1) continued development of the "PKB" object-oriented research database, 2) development of MMDB, a 3-dimensional structure database for modeling applications, and 3) development of MMDB-API, an applications programming interface. PKB has been modified to include explicit ensemble and correlated disorder models parsed from Protein Data Bank (PDB) files, subject to validation checks, so that this information may be incorporated into MMDB. Stable structure identifiers are also now being assigned, as required for stable research data set identification and MMDB incremental update. MMDB is an ASN.1 database whose specification defines precisely the covalent structure of biopolymers and non-polymer components and an unambiguous mapping to 3- dimensional coordinates. Several new validation checks have been incorporated into MMDB, including flags for anomalous bonding and chirality in "standard" groups, correction of anomalous atomic symbol usage in frequent cases, and omission clearly erroneous PDB bonding data. Cross references to NCBI sequence databases and Medline have also been added to MMDB, and PDB-derived sequences for "Entrez" are now produced directly from it. The MMDB database itself is now distributed as the searchable "Structure" database in network and world-wide-web Entrez. MMDB-API is an in-memory data structure populated automatically from MMDB files and an associated function library in C. It has been used to produce Kinemage and PDB report generators for Entrez, and a beta version of an Entrez graphics viewer. The significance of this work is in providing biologists with easy access to structural data and information on known sequence-structure relationships, and in providing a software infrastructure to developers of molecular modeling software.

我们已经开发了用于分子建模的数据库和软件 和序列结构关系分析。 这些工具 免费分发给生物学家和生物技术开发人员 软件 工作主要集中在三个方面：1）继续发展 “PKB”面向对象研究数据库的开发; 2）内存数据库的开发; 用于建模应用的三维结构数据库，以及3） 开发MMDB-API，一个应用程序编程接口。 PKB有 被修改为包括明确的合奏和相关的障碍模型 从蛋白质数据库（PDB）文件解析，经过验证检查， 从而可以将该信息合并到MMDB中。稳定结构 根据稳定研究的需要，现在也正在分配标识符 数据集标识和内存数据库增量更新。 MDB是一个ASN。1 数据库，其规格精确定义了 生物聚合物和非聚合物组分，并明确映射到3- 空间坐标 已经进行了几项新的验证检查， 包含在MMDB中，包括异常绑定的标志， “标准”基团中的手征性，异常原子符号的校正 在频繁的情况下使用，并省略明显错误的PDB绑定数据。 对NCBI序列数据库和Medline的交叉引用也已经被公开。 已添加到MMDB，现在已生成PDB派生的“Zeroz”序列 MMDB数据库本身现在作为 可在网络和万维网上搜索的“结构”数据库。 MMDB-API是一种内存中的数据结构，它从MMDB自动填充 文件和相关的C函数库。 它已被用于 制作Kinemage和PDB报告生成器，以及一个测试版 一个图形浏览器。 这项工作的意义在于 为生物学家提供了获取结构数据和信息的便捷途径 已知的序列结构关系，并提供一个软件 分子建模软件的开发者。