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PDB Deposition is a new deposition tool developed by the wwPDB partners. It supports X-ray, NMR and EM structures.
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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.
Group Depositions are sets of related PDB entries deposited at the same time. PDB entries belonging to each group are available by clicking on the Group ID.
Chemical Component entries
All Chemical Component entries defined in Chemical Component dictionary are listed.
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Latest entries provides the list of latest released entries 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.
NMR data search (BMRB)
NMR data search (BMRB) is a service to search BMRB entries in the biomolecule NMR database BMRB.
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.
Status Search is a service to search PDB entries which are already deposited but have not been released yet.
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.
Yorodumi is a website to easily watch, move, rotate, learn, and enjoy 3D structures of biological molecules.
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NMRToolBox is composed of various tools for spectral assignment and analysis
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.
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.
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).
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.
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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.
Molecule of the month
Introduction to biological macromolecules written by Dr. David S. Goodsell of RCSB...
Materials used in the previous workshop and tutorials are available from this site.
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.
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.
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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.
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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.
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PDB format - PDBx/mmCIF conversion
PDB format - PDBx/mmCIF conversion is a tool for converting into PDB format and mmCIF, respectively.