The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of proteins, nucleic acids, and other biological macromolecules with a 25 year history of service to a global community. PDB is being replaced by 3DB, the Three-Dimensional Database of Biomolecular Structures that will continue to operate from Brookhaven National Laboratory. 3DB will be a highly sophisticated knowledge-based system for archiving and accessing structural information that combines the advantages of object oriented and relational database systems. 3DB will operate as a direct-deposition archive that will also accept third-party supplied annotations. Conversion of PDB to 3DB will be evolutionary, providing a high degree of compatibility with existing software.
With a few keystrokes and mouse button clicks on a UNIX workstation, the entire Protein Data Bank archive is now available for searching and displaying the three-dimensional protein structures contained within.
This paper describes the design and full implementation of a new concept in data deposition and validation: AutoDep (copyright Brookhaven Science Associates LLC). AutoDep changes the traditional procedure for data acceptance and validation of the primary databases into an interactive depositor-driven operation which almost eliminates the delay between the acceptance of the data and its public release. The system takes full advantage of the knowledge and expertise of the experimenters, rather than relying on the database curators for the complete and accurate description of the structural experiment and its results. AutoDep, developed by the Protein Data Bank at Brookhaven National Laboratory (BNL) as a¯exible and portable system, has already been adopted by other primary databases and implemented on different platforms/operating systems. AutoDep was introduced
A multi-laboratory ontology construction effort during the summer and fall of 2009 prototyped an ontology for counterfeit semiconductor manufacturing. This effort included an ontology development team and an ontology validation methods team. Here the third team of the Ontology Project, the Data Analysis (DA) team reports on their approaches, the tools they used, and results for mining literature for terminology pertinent to counterfeit semiconductor manufacturing. A discussion of the value of ontology-based analysis is presented, with insights drawn from other ontology-based methods regularly used in the analysis of genomic experiments. Finally, suggestions for future work are offered.
This paper describes the conformational features of 6-> I hydrogen bonded tums (n:-turns) observed in proteins and peptides. The polypeptide conformations under the constraint of 6-> 1 hydrogen bond were selected from Brookhaven Protein Data Banlc (PDB) using a FORTRAN program developed in our laboratory. The data set consisted of the co-ordinates of 228 non-homologous protein chains, detennined by X-ray crystallography to better than 2.5 A resolution. Totally 486 n:-turns were located. 367 n:-Tums
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