DATABASES FOR MOLECULAR MODELING

分子建模数据库

• 批准号: 3781279
• 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/3781279
• 关键词: chemical models; computer assisted sequence analysis; computer program /software; computer simulation; computer system design /evaluation; information systems; physical model; protein sequence; protein structure

We have developed databases and software useful for modeling of protein three-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 GenBank entries describing proteins and nucleic acids with known structure, and 3) design and implementation of a structural database convenient for developers of molecular modeling software. The PKB data specification has been expanded to include all data items defined by the Protein Data Bank, including scientific literature citations and bonded connectivity. We have also added validation procedures which recover correct definitions of biopolymer sequence and chemical modification, and identify stereochemical anomalies. We have used PKB to produce ASN.1-language reports of structural features mapable to sequence, using the current NCBI/GenBank data specification. These data have been updated as new structures became available from the Protein Data Bank, and incorporated into the widely distributed GenBank/ASN.1 and Entrez databases. To provide convenient access to structural data from modern application programs written in C we have begun development of an ASN.1 database containing complete covalent and spatial structure data. Its specification allows comparison of biopolymer or non-biopolymer components of biological macromolecules according to chemical structure, and direct representation of three-dimensional structure inferred by alignment with homologous or chemically similar molecules. 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.

我们已经开发了用于蛋白质建模的数据库和软件 三维结构与层序结构分析 关系。这些工具已经免费分发给生物学家 和生物技术软件的开发者。 工作可分为 三个方面：1）继续开发“PKB”面向对象 研究数据库，2）产生描述蛋白质的GenBank条目 和具有已知结构的核酸，以及3）设计和实施 一个结构数据库，方便分子建模的开发人员 软件 PKB数据规范已扩展到包括所有 蛋白质数据库定义的数据项，包括科学 文献引用和键合连接。 我们还增加了 恢复生物聚合物的正确定义的验证程序 序列和化学修饰，并确定立体化学 异常 我们已经使用PKB生成ASN.1语言报告， 可映射到序列的结构特征，使用当前NCBI/GenBank 数据规格 这些数据已更新为新结构 从蛋白质数据库中获得，并纳入了 广泛分布于GenBank/ASN.1和GenBank/ASN.2数据库中。 提供 从现代应用程序方便地访问结构数据 我们已经开始开发一个ASN.1数据库， 完整的共价键和空间结构数据。其规格允许 生物制品的生物聚合物或非生物聚合物组分的比较 大分子根据化学结构，并直接 通过比对推断的三维结构的表示， 同源或化学相似的分子。 其意义 工作是为生物学家提供方便的结构数据， 为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