Table 1.
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.