DATABASES FOR MOLECULAR MODELING

我们已经开发了用于蛋白质建模的数据库和软件 3-三维结构和序列-结构关系分析。 这些工具已免费分发给生物学家和 生物技术软件这项工作可分为三个方面：1） 继续开发“pKB”面向对象的研究数据库，2） 用于蛋白质和核酸的“BZ”序列的产生， 已知结构，以及3）MMDB的实现，三维 已修改了“PKB”结构数据库，以包括核心” 模体识别、非冗余集构造和鲁棒输入 蛋白质数据库（PDB）文件包含新的错误类别。它有 用于生成结构特征的ASN.1语言报告 可映射到序列，根据“Zeroz”的需要，使用NCBI/GenBank 序列数据规范。包括明确的三维 我们在“MLDB”中创建了MMDB数据库。MMDB采用 精确定义化学图的数据规范 生物聚合物和非聚合物组分如底物或辅因子， 并将它们映射到一个测量过的三维空间中。用这样的方式来 便于广义同源建模、空间结构的推断 基于化学结构的比较和排列。MMDB提供 数据的形式方便“Zeroz”和分子的开发人员 建模软件，如ASN.1数据文件和相关的对象加载器 它自动生成类似的内存中的C数据结构。 化学图主要是通过pKB中的计算构建的，因为 此信息隐含在当前PDB格式中，我们有 验证了使用的算法。这项工作的意义在于 为生物学家提供了方便的结构数据， 为感兴趣的研究人员提供软件基础设施， 序列-结构关系和程序员开发分子 建模软件

We have developed databases and software useful for modeling of protein 3-dimensional structure and analysis of sequence-structure relationships. These tools have been distributed freely to biologists and developers of biotechnology software. The work may be divided into three areas: 1) continued development of the "pKB" object-oriented research database, 2) production of "Entrez" sequences for proteins and nucleic acids with known structure, and 3) implementation of a MMDB, a 3-dimensional structure database for "Entrez", PKB has been modified to include core" motif identification, non-redundant set construction, and robust input of protein Data Bank (PDB) files containing new classes of error. It has been used to produce ASN.1-language reports of structural features mappable to sequence, as needed for "Entrez", using the NCBI/GenBank sequence data specification. To include explicit 3-dimensional information in "Entrez" we have created the MMDB database. MMDB employs an ASN.l data specification which defines precisely the chemical graph of biopolymers and non-polymer components such a substrates or cofactors, and maps them into a measured 3-dimensional space. It in this way facilitates generalized homology modeling, inference of spatial structure based on comparison and alignment by chemical structure. MMDB provides data in a form convenient for "Entrez" and for developers of molecular modeling software, as ASN.1 data files and associated object loaders which automatically generate analogous in-memory C data structures. Chemical graphs are constructed largely by computation within pKB, since this information is implicit within the current PDB format, and we have validated the algorithms used. The significance of this work is in providing biologists with easy access to structural data, and in providing a software infrastructure to researchers interested in sequence-structure relationships and programmers developing molecular modeling software.