No. 16
Winter 2003

Front Page

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PDB Deposition Statistics for 2002

PDB Focus: Sequence Prerelease

New PDB Mirror Site in Germany

Rsync Script for FTP Mirroring

Theoretical Models Search Interface on the PDB Beta Web Site

BioEditor Now Available from the PDB Web Site

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PDB Paper Published in Bioinformatics

"Banking on Structures": BioIT World Article Looks at the PDB

PDB Art Exhibit Part of CCMB's Silver Jubilee Celebrations and Symposium

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PDB Annual Report 2002 Now Available

PDB CD-ROM Set #102 and Subsequent Releases

PDB Focus: Educational Resources at the PDB

PDB Molecules of the Quarter: Dihydrofolate Reductase, Ferritin and Transferrin, and Cytochrome c

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© 2003 PDB


PDB Paper Published in Bioinformatics

The September 2002 issue of Bioinformatics contains a paper describing the Ontology Driven Architecture that was developed to increase efficiency in the use of macromolecular structure (MMS) data contained in the PDB. The paper describes the OpenMMS Toolkit, a suite of software tools that conform to the OMG/LSR Corba standard (OMG specification formal/02-05-01). The OpenMMS Toolkit is based on a metamodel architecture and is written entirely in Java. It contains an mmCIF parser, reference and database Corba servers, a relational database loader and a prototype XML formatted file converter. Detailed documentation and all of the source code are available at

D.S. Greer, J.D. Westbrook, P.E. Bourne (2002): An ontology driven architecture for derived representations of macromolecular structure. Bioinformatics, 18(9), pp. 1280-1281. ? Oxford University Press.