DATABASES FOR MOLECULAR MODELING

我们已经开发了用于分子建模的数据库和软件

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.