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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 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]