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

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.