title: Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures.
abstract: The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the Resource Description Framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.
authors: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan akinjo@protein.osaka-u.ac.jp.
authors: Akira R
authors: AR
authors: Kinjo
authors: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors: Gert-Jan
authors: GJ
authors: Bekker
authors: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors: Hirofumi
authors: H
authors: Suzuki
authors: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors: Yuko
authors: Y
authors: Tsuchiya
authors: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors: Takeshi
authors: T
authors: Kawabata
authors: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors: Yasuyo
authors: Y
authors: Ikegawa
authors: Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan.
authors: Haruki
authors: H
authors: Nakamura
mesh_terms: D030562:Databases, Protein; D007564:Japan; D008958:Models, Molecular; D011487:Protein Conformation; D012984:Software; D013329:Structure-Activity Relationship; D014584:User-Computer Interface; D064878:Web Browser