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Table 1 Useful tools and resources for protein family, domain and motif analysis

From: Tools and resources for identifying protein families, domains and motifs

Database Description URL Published reference
Blocks Database of protein alignment blocks [19]
CDD Conserved domain database [47]
CluSTr Clusters of SWISS-PROT and TrEMBL proteins [34]
DOMO Protein-domain database based on sequence alignments [24]
InterPro Integrated documentation resource for protein families, domains and functional sites [49]
IProClass Integrated protein classification database [45]
MetaFam Database of protein family information [43]
Pfam Collection of multiple sequence alignments and hidden Markov models [13]
PIR Protein Information Resource [4]
PIR-ALN Curated database of protein sequence alignments [26]
PRINTS-S Compendium of protein fingerprints [11]
ProClass Non-redundant protein database organized by family relationships [28]
ProDom Automatic compilation of homologous domains [21]
PROSITE Database of patterns and profiles describing protein families and domains [9]
ProtoMap Automatic hierarchical classification of SWISS-PROT proteins [30]
SBASE Curated protein domain library based on sequence clustering [51]
SMART Simple Modular Architecture Research Tool - a collection of protein families and domains [15]
SWISS-PROT and TrEMBL Protein sequence databases or [2]
SYSTERS Systematic re-searching method for sequence searching and clustering [32]
TIGRFAMs Protein families based on hidden Markov models [17]