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PDB Deposition
PDB Deposition
PDB Deposition is a new deposition tool developed by the wwPDB partners. It supports X-ray, NMR and EM structures.
PDB, BMRB, EMDB, deposition, NMR, electron microscopy
PDBj Mine
PDBj Mine
PDBj Mine is a new generic interface to search PDB entries by PDB ID and keyword etc. See also Basic Usage.
PDB, 3D structure, search, chemical component
Advanced Search (PDBj Mine)
Advanced Search (PDBj Mine)
Advanced Search is an advanced interface to search PDB entries by a combination of various conditions.
PDB, 3D structure, search, chemical component
Large Structures
Large Structures
Large Structures are large structure entries which exceed the limitations of the original PDB file format and are released as a single entry without being split into multiple entries.
PDB, 3D structure, search
Chemie search
Chemie search
Chemie search can be used to search the chemical component database which is part of the PDB.
chemical component, search, 3D structure, viewer
NMR data search (BMRB)
NMR data search (BMRB)
NMR data search (BMRB) is a service to search BMRB entries in the biomolecule NMR database BMRB.
BMRB, NMR
Sequence Navigator
Sequence Navigator
Sequence Navigator is a tool to look for molecules with similar sequences.
sequence, search, similarity
EM Navigator
EM Navigator
EM Navigator is a data browser for biological 3D electron microscopy.
EMDB, electron microscopy, search, 3D structure
wwPDB/RDF
wwPDB/RDF
wwPDB/RDF is a collection of PDB data in the Resource Description Framework (RDF) format. The RDF format is the standard format for the Semantic Web. An ontology defined in the Web Ontology Language (OWL) is also provided for the PDB/RDF, which is a straightforward translation of the PDB mmCIF Exchange Dictionary.
PDB, chemical component
SeSAW
SeSAW
SeSAW (Sequence-Derived Structural Alignment Weights) provides functional annotations that identifies conserved sequence and structural motifs in query proteins. See also SeSAW Tutorial.
sequence, 3D structure, function prediction
Ligand Binding Sites (GIRAF)
Ligand Binding Sites (GIRAF)
GIRAF is a similarity search service for ligand binding sites available at this site. For a given PDB ID or uploaded PDB file, GIRAF searches for known ligand binding sites in the PDB that are similar to substructures of the query.
chemical component, binding site, similarity
Latest Release Search
Latest Release Search
Latest Release Search is a service to search latest released entry list including both newly registered entries and updated entries. Each entry ID is linked to the PDBj Mine page. All the entry ID list in PDB is also available.
PDB, search
Status Search
Status Search
Status Search is a service to search PDB entries which are already deposited but have not been released yet.
PDB, search
jV (PDBj Viewer)
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.
viewer, 3D structure, PDB
Molmil
Molmil
Molmil is a new high performance molecular viewer developed by PDBj using modern web technology for optimal integration and user experience. It can be used for visualization of proteins, nucleic acids and chemical compounds present in PDB (flat), mmCIF, PDBML and the PDBj developed format mmJSON. It also supports saving PNG images of high resolution and runs inside modern web-browsers without any need for plugins.
3D structure, viewer
Yorodumi
Yorodumi
Yorodumi is a website to easily watch, move, rotate, learn, and enjoy 3D structures of biological molecules.
PDB, EMDB, chemical component, 3D structure, viewer
ASH
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.
similarity, search, 3D structure
MAFFTash
MAFFTash
MAFFTash is a tool that calculates multple sequence alignments from sequences and structures.
similarity, search, 3D structure, sequence
NMRToolBox
NMRToolBox
NMRToolBox is composed of various tools for spectral assignment and analysis
NMR, search
CRNPRED
CRNPRED
CRNPRED is a web-based service that predicts one-dimensional protein structures including secondary structures, contact numbers, and residue-wise contact orders from amino acid sequence.
secondary structure, 3D structure, structure prediction
Spanner
Spanner
Spanner is a structural homology modeling program?that is, it threads a specific amino-acid sequence onto a specific PDB structure, patching up the gaps as best it can.
secondary structure, 3D structure, structure prediction
SFAS
SFAS
SFAS (Sequence to Function Annotation Server) is a web-based tool for predicting the structure of an amino acid sequence. SFAS runs several external programs for sequence alignment and structural modeling and organized their results. SFAS does not do any complicated calculations. There are currently several choices for alignment and one choice for structural modeling. In the future, the number of choices will be increased.
secondary structure, 3D structure, structure prediction
eF-site
eF-site
eF-site (electrostatic-surface of Functional site) is a database for molecular surfaces of proteins' functional sites, displaying the electrostatic potentials and hydrophobic properties together on the Connolly surfaces of the active sites, for analyses of the molecular recognition mechanisms.
3D structure, function prediction, surface structure
eF-surf
eF-surf
eF-surf is a web server to calculate the molecular surface of the up-loaded file with PDB format in the same way as the eF-site database.
3D structure, function prediction, surface structure
eF-seek
eF-seek
eF-seek is a web server to search for the similar ligand binding sites for the uploaded coordinate file with PDB format. The representative binding sites in eF-site database are search by our own algorithm based on the clique search algorithm.
search, 3D structure, function prediction, surface structure
ProMode Elastic
ProMode Elastic

ProMode Elastic is a database of normal mode analysis of PDB data. The normal mode analysis is performed by the program PDBETA we have developed. PDBETA is a program of Elastic-network-model based normal mode analysis in Torsional Angle space for PDB data. PDBETA can describe molecular structures with relatively smaller number of degrees of freedom, and take into computation not only proteins but also DNA, RNA, and ligand molecules (hydrogen atoms and water molecules are excluded currently to suppress the number of variables).

3D structure
hGTOP
hGTOP

hGTOP is a database containing annotations of proteins in human, mouse and rat genomes. The annotations are mainly about homologous proteins with known 3D structures as well as other structural information such as predicted (or observed) secondary structures and disordered regions. In addition, for each protein in the above genomes, homologous proteins in the genomes of approximately 170 representative organisms are listed.

sequence, similarity, structure prediction, genome
eProtS
eProtS
eProtS (Encyclopedia of Protein Structures) is a dictionary with pictures of the protein three-dimensional structures, for understanding the tertiary structures and the biological functions for several selected protein molecules that are particularly important for biology. This Web site can be prepared for the general audience. As it is a wiki-based repository of documents, any people can deposit or edit documents as well as browse.
education/dictionary, 3D structure
Molecule of the month
Molecule of the month
Introduction to biological macromolecules written by Dr. David S. Goodsell of RCSB...
education/dictionary, 3D structure
Previous workshop
Previous workshop
Materials used in the previous workshop and tutorials are available from this site.
education/dictionary
PDBj Games
PDBj Games
PDBj Games are a collection of games such as Pelmanism and Snake games through which you can learn about amino acids and proteins, polymers of amino acids.
education/dictionary
Omokage search
Omokage search
Omokage search is a shape similarity search service for 3D structures of macromolecules. By comparing overall shapes, and ignoring details, similar-shaped structures are searched.
PDB, EMDB, electron microscopy, search, 3D structure, similarity
gmfit
gmfit
gmfit is a program for fast fitting of 3D objects using Gaussian mixture model. The fitting service between two EMDB density maps or PDB structures is available through the WEB.
PDB, EMDB, similarity, electron microscopy, 3D structure
HOMCOS
HOMCOS
HOMCOS is a service for searching 3D complex structures in PDB from sequences or chemical structures, and for modeling 3D complex structures based on the found template structures.
PDB, search, 3D structure, structure prediction, chemical component, binding site
Structure Navigator
Structure Navigator
Structure Navigator is a tool to look for molecules with similar structures.
3D structure, search, similarity
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