Acta Crystallographica Section D

Biological Crystallography

Volume 69, Part 5 (May 2013)


short communications



Acta Cryst. (2013). D69, 914-919    [ doi:10.1107/S0907444913001728 ]

Integrated database of information from structural genomics experiments

Y. Asada, M. Sugahara, H. Mizutani, H. Naitow, T. Tanaka, Y. Matsuura, Y. Agari, A. Ebihara, A. Shinkai, S. Kuramitsu, S. Yokoyama, E. Kaminuma, N. Kobayashi, K. Nishikata, S. Shimoyama, T. Toyoda, T. Ishikawa and N. Kunishima

Abstract: Information from structural genomics experiments at the RIKEN SPring-8 Center, Japan has been compiled and published as an integrated database. The contents of the database are (i) experimental data from nine species of bacteria that cover a large variety of protein molecules in terms of both evolution and properties (http://database.riken.jp/db/bacpedia ), (ii) experimental data from mutant proteins that were designed systematically to study the influence of mutations on the diffraction quality of protein crystals (http://database.riken.jp/db/bacpedia ) and (iii) experimental data from heavy-atom-labelled proteins from the heavy-atom database HATODAS (http://database.riken.jp/db/hatodas ). The database integration adopts the semantic web, which is suitable for data reuse and automatic processing, thereby allowing batch downloads of full data and data reconstruction to produce new databases. In addition, to enhance the use of data (i) and (ii) by general researchers in biosciences, a comprehensible user interface, Bacpedia (http://bacpedia.harima.riken.jp ), has been developed.

Keywords: crystal structures; protein crystallography; synchrotron radiation; X-rays; heavy atoms; semantic web.


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[ doi:10.1107/S0907444913001728/mh5084sup1.pdf ]
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