About PDBj services
In PDBj, following services are available.
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Data Deposition
- PDB Deposition (Deposition of X-ray, EM and NMR structures.) [Tutorial]
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Search
- Search PDB (PDBj Mine)
- Search PDB (Advanced Search)
- Large Structures (Search Large Structure entries)
- Chemie search (Search chemical entries)
- Search BMRB ( Search entries in the biomolecule NMR database BMRB )
- Sequence Navigator (Entry search with similar sequences)
- Structure Navigator (Entry search with similar structures)
- EM Navigator (Web service of molecular structure solved by the electron microscopy)
- Omokage search (Shape similarity search of macromolecules)
- wwPDB/RDF (a collection of PDB data in the Resource Description Framework format)
- SeSAW (Service for functional annotation based on both sequence and structure)
- GIRAF (Entry search with similar ligand binding sites)
- Latest Released Search (Search latest released or updated entries)
- Status Search (The status information of deposited data)
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Molecular Viewers
- jV (Graphic Viewer)
- Molmil molecular viewer (WebGL Molecular Viewer)
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Services and Softwares
- Yorodumi (a website to easily watch, move, rotate, learn, and enjoy 3D structures of biological molecules)
- ASH (A calculating program to molecular structural similarity)
- MAFFTash (A tool to calculate molecular similarity considering both sequence and structure)
- NMRToolBox (Useful tools for NMR data evaluation)
- gmfit (A superimposition program of atomic models and 3D density maps)
- CRNPRED (Structure prediction service based on the sequence)
- Spanner (Structure prediction service using structure known molecules with similar sequence)
- SFAS (Multiple service both sequence alignment and structure prediction)
- HOMCOS (Finding and modeling of 3D structures complexes)
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Derived databases
- eF-site (Database for molecular surfaces of their functional sites)
- eF-surf (Calculating the molecular electrostatic potential and surface)
- eF-seek (Searching similar ligand binding sites)
- ProMode Elastic (Database of normal mode analysis of PDB data)
- hGTOP (Database containing annotations of proteins in human, mouse and rat genoms)
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Educational Service
- eProtS (Encyclopedia of protein structures)
- Molecule of the Month (Articles about topical matter related molecules in RCSB, translated into Japanese by PDBj)
- Previous workshop (materials used in the previous workshop)
- PDBj Games
Created: 2016-12-12 (last edited: more than 1 year ago)
