Table 1.
Analysis tools and derived databases
| Service | Description | URLa | Reference |
|---|---|---|---|
| PDBj Mine | Simple, advanced and SQL search for PDB data | pdbj.org/mine | (7) |
| Sequence Navigator | BLAST (22) search against PDB | pdbj.org/seqnavix | – |
| Structure Navigator | ASH structure similarity search | pdbj.org/stnavix | (23) |
| SeSAW | Functional site prediction | pdbj.org/sesaw | (24) |
| GIRAF | Interaction interface similarity search | pdbj.org/giraf | (25–27) |
| EM Navigator | EM structure browser | pdbj.org/emnavi | – |
| jV | Molecular graphics viewer | pdbj.org/jv | (28) |
| Yorodumi | Integrated PDB/EMDB data browser | pdbj.org/yorodumi | – |
| Protein Globe | “Protein universe” browser | pdbj.org/globe | (2) |
| ASH | Pairwise structure alignment | pdbj.org/ash | (23,29,30) |
| MAFTTash | Integrated multiple sequence/structure alignment | pdbj.org/mafftash | (31) |
| CRNPRED | One-dimensional structure prediction | pdbj.org/crnpred | (32,33) |
| Spanner | Homology modeling | pdbj.org/spanner | (34) |
| SFAS | Automated function annotation | pdbj.org/sfas | – |
| eF-site | Electrostatic surface database | pdbj.org/ef-site | (28,35) |
| eF-seek | Search against eF-site | pdbj.org/ef-seek | (36) |
| eF-surf | Building electrostatic surfaces | pdbj.org/ef-surf | (36) |
| ProMode | Database of normal mode analyses of proteins | pdbj.org/promode | (37) |
| ProMode Elastic | ProMode with elastic network model | pdbj.org/promode_elastic | – |
| ProMode Oligomer | ProMode for oligomeric proteins | pdbj.org/promode_oligomer | – |
| eProtS | Educational articles on protein structures | pdbj.org/eprots | – |
| Molecule of the Month | Japanese translation of RCSB PDB MoM | pdbj.org/mom | (3) |
aThe ‘http://’ prefix is omitted.