AutoDep: a web-based system for deposition and validation of macromolecular structural ­information

• Published in: Acta crystallographica. Section D, Biological crystallography. Biological crystallography., 2000-07, Vol.56 (7), p.828-841
• Main Authors: Lin, Dawei, Manning, Nancy O., Jiang, Jiansheng, Abola, Enrique E., Stampf, David, Prilusky, Jaime, Sussman, Joel L.
• Format: Article
• Language: English
• Subjects: AutoDep; CIF; Computer Security; Database Management Systems; deposition; Internet; Macromolecular Substances; PDB; User-Computer Interface; validation; Vocabulary; World Wide Web
• ISSN: 1399-0047; 0907-4449; 1399-0047
• DOI: 10.1107/S0907444900005655

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 flexible and portable system, has already been adopted by other primary databases and implemented on different platforms/operating systems. AutoDep was introduced at BNL in 1996 [see Manning (1996), Protein Data Bank Quart. Newslett.77, 2 (ftp://ftp.rcsb.org/pub/pdb/doc/newsletters/bnl/newsletter96jul/newslttr.txt); Manning (1996), Protein Data Bank Quart. Newslett.78, 2 (ftp://ftp.rcsb.org/pub/pdb/doc/newsletters/bnl/newsletter96oct/newslttr.txt)].