Table 1.
List of databases/programs in PIPA
| Method/Database | Description | Website* |
| CatFam | Enzyme profile databases based on three- and four-digit EC numbers | developed by our group |
| CDD | NCBI Conserved Domains Database | [9] |
| COG | Clusters of Orthologous Groups of proteins | [39] |
| Pfam+ | Hidden Markov Models of protein domains and families | [40] |
| TIGRfam+ | Hidden Markov Models of curated protein families | [41] |
| SMART+ | Identification and annotation of genetically mobile domains | [42] |
| Gene3D+ | Protein families with structural information | [43] |
| FprintScan+ | Program that searches the protein fingerprint database PRINTS | [44] |
| PANTHER+ | Proteins classified by experts into families and subfamilies | [45] |
| SUPERFAMILY+ | Structural assignments to protein sequences at the superfamily level | [46] |
| ProDom+ | Automatically generated protein domain families | [47] |
| PIR+ | Integrated Protein Informatics Resource | [48] |
| PROSITE+ | Database of protein domains, families and functional sites | [49] |
| COILS+ | Prediction of coiled-coil regions in proteins | [50] |
| Phobius | A combined transmembrane topology and signal peptide predictor | [51] |
| PSORTb | Prediction of the subcellular localization of bacterial proteins | [52] |
*Accessed on July 13, 2007
+Integrated from InterPro
PIPA currently integrates 16 programs/databases that are either developed by our group (CatFam) or publicly available.