http://pdbj.org/

http://wwpdb.org/

Licensed under a Creative Commons
表示 2.1 日本 license (c)2015

Abstract
The Protein Data Bank Japan (PDBj, http://pdbj.org/) is a member of the worldwide Protein

Since 2001, PDBj has been managed at Institute for Protein Research, Osaka University as a member of the wwPDB, to curate, edit and process the deposited data
for and open, public, and single archive of the wwPDB. The PDB archive contains more than 110,000 entries now.

Data Bank (wwPDB: http://wwpdb.org/) [1,2]. PDBj accepts and processes experimental
macromolecular structure data determined by X-ray crystallography, SAXS/SANS, NMR, andElectron Microscopy as a Data-in service. While maintaining the archive in collaboration withother wwPDB partners, PDBj also provides a wide range of Data-out services and tools foranalyzing structures and functions of proteins, as shown in Table 1.

● “Data-in” activitiy, common in all the wwPDB members withTo facilitate the integration of structure data with other life sciences data resources, we havedeveloped data in formats compatible with semantic web technologies: PDB/RDF(http://rdf.wwpdb.org/) and Chem_Comp/RDF (http://rdf.wwpdb.org/cc/ ), PDB and chemical

PDBj staﬀs(April, 2015)

compounds data in the Resource Description Framework (RDF) format, along with its
ontology in Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary

PDBj-BMRB staﬀ

[1,2]. NMR experimental data in BMRB database are also being described in RDF as

high quality control. For that purpose, new format, data deposition,and validation system are developed.
● “Data-out” services, characteristic at each wwPDB member site
except common ftp-site data.
Processed total at PDBj (25,392, 23 SEP 2015)
120000100000BMRB/RDF, and those data are integrated thorough the linked-data technology.

Burley SK

All available PDB data (112,387, 23 SEP 2015)

80000

PDBj curates and processes

about a quarter of the depositeddata, mainly from Asian region.

wwPDB members andtheir heads

60000
40000
20000
02000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015** 23 SEP 2015

Molmil viewer for molecular surfacesof large structures

Molmil: Molcular Viewer based on WebGL・Based on JavaScript/WebGL.
・Supports PDB, mmCIF, PDBML formats.
・Links to PDB, chem_comp（Compound), and ProMode Elastic.
・Outputs screenshots.

Coat protein of virus (180 chains, 2.5 MDa)

Integration of EMDB:
similar
SHAPE
Integration Searchwith EMDB:forSearchfor similar
SHAPE
Query: human RNA polymerase II with RNA (EMDB: 2190)
Similar shapes from 195,658 images“Omokage” Search

GIRAF:
Similar binding sites

EM Navi:
EMDB browser

eF-site:Mol. Surface DB

eF-seek:
Similar surfaces

Yorodumi:
PDB & EMDBProMode:Normal Modes

PDBj-BMRB (BioMagResBank)

Web-sites for NMR database managed by PDBj -BMRB
Data deposition

Data publication

January 2014 -validation data for all X-ray
structures has made publicly available
through the wwPDB ftp sites

Current Canonical PDB format : PDBx/mmCIF・PDB format is almost 40 years old and does not support today’ s science.
・PDB Record format limitations-Max. 62 chains-Max 99.999 atoms-No bond orders or chirality speciﬁed for ligands-No support for NMR, EM hybrid methods,...
-Meta-data speciﬁcation cumbersome and inﬂexible

・Preserve backward compatibility where possible web service
to create PDB format data ﬁles・Near future, it will be ﬁnished to provide PDB data in legacy PDB format
PDB format
SMSdep

ADIT-NMRBMRB mirror

PDBj-BMRB portal

MagRO-NMRView toolfor NMR data analysis
and Deposition to BMRB

mmCIF

ﬁt_robot: tool for extraction of ordered region
in NMR structure ensemble
Multidimensional
scaling andclustering

Two distinctive
clusters of residues

PDBx/mmCIF Software Support
http://mmcif.wwpdb.org/

2.5

21.5
10.5
0-2.5

-1.5-0.5

0.5-0.5-1-1.5-2-2.5

Inter atomic distancevariance matrix

BMRBxTool, BMRBoTool:
tools for conversion of BMRB entries
to XML and RDF format

1.5

2.5

Phenix and Refmac – produce native PDBx ﬁles for deposition
MMDB - macromolecular object library in CCP4
iotbx.cif/ucif - CCTBx C++/Python IO library with dictionary validation
CCIF – CCP4 C++ library with FORTRAN support and dictionary validation
CBFLib - ANSI-C library for CIF & imgCIF ﬁles
mmLIB - Python toolkit supporting CIF & mmCIFBioPython - Python toolkit for computational biology
PyCifRW - Python CIF/mmCIF parsing tools
BioJava - Java mmCIF IO package
STAR::Parser – Perl mmCIF parser and molecular object library
RCSBTools - C++/Python parsing and dictionary validation tools plus manyother supporting format conversion and data management applications• Visualization - Chimera, Jmol, OpenRasMol•••••••••••