Outcome of a workshop on archiving structural models of biological macromolecules.
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Genomics↗
Biomedical subjects
John D Westbrook
Publications and source records attributed to John D Westbrook.
Report of the working group on crystal phase identifiers.
The proposed crystalline phase identifier consists of a number of components (layers) describing enough properties of the phase to allow a unique identification. These layers consist of the chemical formula, a flag indicating the state of matter, the space-group number and the Wyckoff sequence. They are defined in such a way that they can be incorporated into the IUPAC International Chemical Identifier (InChI) proposed by the International Union of Pure and Applied Chemistry (IUPAC).
Journal Article↗
Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank.
The RCSB Protein Data Bank (PDB) has a number of options for deposition of structural data and has developed software tools to facilitate the process. In addition to ADIT and the PDB Validation Suite, a new software application, pdb_extract, has been designed to promote automatic data deposition of structures solved by X-ray diffraction. The pdb_extract software can extract information about data reduction, phasing, molecular replacement, density modification and refinement from the output files produced by many X-ray crystallographic applications. The options, procedures and tools for accurate and automated PDB data deposition are described here.
Automation↗
The impact of structural genomics on the protein data bank.
The advent of structural genomics presents new challenges to the archive of biomacromolecular structures--the Protein Data Bank (PDB). As technologies involved in structure determination have advanced, both the number and size of structures available in the PDB have increased rapidly. The structural genomics initiatives are creating a large amount of data that needs to be tracked, archived, and made easily available. The PDB has developed tools to facilitate the rapid deposition of data produced by the structural genomics initiatives and has created databases to track the progress of the work.
Animals↗
The PDB format, mmCIF, and other data formats.
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Computational Biology↗
The Protein Data Bank.
The Protein Data Bank [PDB; Berman, Westbrook et al. (2000), Nucleic Acids Res. 28, 235-242; http://www.pdb.org/] is the single worldwide archive of primary structural data of biological macromolecules. Many secondary sources of information are derived from PDB data. It is the starting point for studies in structural bioinformatics. This article describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource. The reader should come away with an understanding of the scope of the PDB and what is provided by the resource.
Databases, Protein↗
An ontology driven architecture for derived representations of macromolecular structure.
UNLABELLED: An object metamodel based on a standard scientific ontology has been developed and used to generate a CORBA interface, an SQL schema and an XML representation for macromolecular structure (MMS) data. In addition to the interface and schema definitions, the metamodel was also used to generate the core elements of a CORBA reference server and a JDBC database loader. The Java source code which implements this metamodel, the CORBA server, database loader and XML converter along with detailed documentation and code examples are available as part of the OpenMMS toolkit. AVAILABILITY: http://openmms.sdsc.edu CONTACT: dsg@sdsc.edu
Database Management Systems↗