PDBj Help

Japanese version:PDBj Help

This page, PDBj Help, provides documentations and tutorials for various services provided by PDBj, Protein Data Bank Japan. They include

• Getting entries;
• Keyword search;
• More advanced search;
• Sequence homology search;
• Structure similarity search;

and more. Refer to Basic Usage to find out basic methods to use PDBj services.

• About PDBj
• Searching services and Software
• PDB entry search (xPSSS)
• Sequence Navigator
• Structure Navigator
• EM Navigator
• jV (PDBj Viewer)
• Protein Globe
• ASH
• Data deposition
• ADIT
• ADIT-NMR
• Related databases and services
• BMRB
• eF-site
• eF-surf
• eF-seek
• eProtS
• ProMode
• Molecule of Month

About PDBj

PDBj stands for the Protein Data Bank Japan. From the PDBj website, one can access macromolecular structures, deposit experimental data, and also make use of a variety of structural bioinformatics web services. PDBj is a member of the Worldwide PDB. PDBj's services are mostly based on the XML (extensible markup language) files called pdbMLplus which is in turn based on PDBML.

Searching services and Software

PDB entry search (xPSSS)

xPSSS is a tool to search PDB entries by PDB ID and keyword etc. See also Basic Usage.

Sequence Navigator

Sequence Navigator is a tool to look for molecules with similar sequences.

Structure Navigator

Structure Navigator is a tool to look for molecules with similar structures.

EM Navigator

EM Navigator is a data browser for biological 3D electron microscopy.

jV (PDBj Viewer)

jV is an interactive 3D viewer program to visualize structure of protein and nucleic acid molecules. This program is also possible to use jV3 on a web browser as a Java applet.

Protein Globe

Protein Globe is a graphical interface to the PDBj and other services. This service uses jV as a Java applet, so the jV available environment is required to use it.

ASH

ASH is a program to perform three-dimensional structure alignment. From the ASH homepage you can run the program over the web or download the software for free.

Data deposition

ADIT

ADIT is used for submitting protein structural information to PDB, Protein DataBank, by a web browser. For the deposition of structures determined by NMR, use ADIT-NMR.

ADIT-NMR

ADIT-NMR is used for submitting protein structural information determined by NMR to PDB and BMRB by a web browser.

Related databases and services

BMRB

NMR database for biomolecules.

eF-site

Electrostatic surface of functional sites.

eF-surf

Electrostatic potential and molecular surface calculating service.

eF-seek

Similar ligand binding sites serching service.

eProtS

eProtS stands for Encyclopedia of Protein Structures. This is a wiki-based repository of documents describing protein structures. Intended for the general audience.

ProMode

Database of normal mode analysis of proteins.

Molecule of Month

Introduction of molecules produced by Dr. David S. Goodsell of RCSB. A new article will be uploaded once a month. The original site of RCSB is here. The Japanese site translated in PDBj is here.

Questions and Comments

forPDBjMember