Table 1.
Useful tools and resources for protein family, domain and motif analysis
| Database | Description | URL | Published reference |
| Blocks | Database of protein alignment blocks | http://blocks.fhcrc.org | [19] |
| CDD | Conserved domain database | http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml | [47] |
| CluSTr | Clusters of SWISS-PROT and TrEMBL proteins | http://www.ebi.ac.uk/clustr/ | [34] |
| DOMO | Protein-domain database based on sequence alignments | http://www.infobiogen.fr/services/domo/ | [24] |
| InterPro | Integrated documentation resource for protein families, domains and functional sites | http://www.ebi.ac.uk/interpro/ | [49] |
| IProClass | Integrated protein classification database | http://pir.georgetown.edu/iproclass/ | [45] |
| MetaFam | Database of protein family information | http://metafam.ahc.umn.edu/ | [43] |
| Pfam | Collection of multiple sequence alignments and hidden Markov models | http://www.sanger.ac.uk/Software/Pfam/ | [13] |
| PIR | Protein Information Resource | http://pir.georgetown.edu/ | [4] |
| PIR-ALN | Curated database of protein sequence alignments | http://pir.georgetown.edu/pirwww/dbinfo/piraln.html | [26] |
| PRINTS-S | Compendium of protein fingerprints | http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/ | [11] |
| ProClass | Non-redundant protein database organized by family relationships | http://pir.georgetown.edu/gfserver/proclass.html | [28] |
| ProDom | Automatic compilation of homologous domains | http://prodes.toulouse.inra.fr/prodom/doc/prodom.html | [21] |
| PROSITE | Database of patterns and profiles describing protein families and domains | http://www.expasy.ch/prosite/ | [9] |
| ProtoMap | Automatic hierarchical classification of SWISS-PROT proteins | http://www.protomap.cs.huji.ac.il/ | [30] |
| SBASE | Curated protein domain library based on sequence clustering | http://www3.icgeb.trieste.it/~sbasesrv/ | [51] |
| SMART | Simple Modular Architecture Research Tool - a collection of protein families and domains | http://smart.embl-heidelberg.de/ | [15] |
| SWISS-PROT and TrEMBL | Protein sequence databases | http://www.ebi.ac.uk/swissprot/ or http://www.expasy.org/sprot/ | [2] |
| SYSTERS | Systematic re-searching method for sequence searching and clustering | http://systers.molgen.mpg.de/ | [32] |
| TIGRFAMs | Protein families based on hidden Markov models | http://www.tigr.org/TIGRFAMs/ | [17] |