Table 3. Major Protein Domain Collections and Servers
Domain and Motif Collections (Sequence Profiles and Signatures)
Name Website Domains Generation PTP Domain Accession #
PROSITE http://expasy.ch/prosite 1676 Semi-manual PS50055
PRINTS http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/ 1700 Semi-manual PR00700
SMART http://smart.embl-heidelberg.de/ 639 Semi-manual SM00194
PfamA http://www.sanger.ac.uk/Software/Pfam/ 7255 Semi-manual PF00102
PfamB http://www.sanger.ac.uk/Software/Pfam/ 88000 Automatic ---
PRODOM1 http://prodes.toulouse.inra.fr/prodom/doc/prodom.html 579477 Automatic PD000167
BLOCKs1 http://blocks.fhcrc.org/blocks-bin/kidofwais.pl 2101 Automatic PB000242
1)Provides ungapped alignments (i.e. motifs). Rarely encompassses the full-length sequence of conseved domains.
Domain Servers (Useful for Annotation of Sequences)
Name Website Comments
InterProScan http://www.ebi.ac.uk/InterProScan/ Searches many domain databases simultaneously
CD server http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi Output includes E-values and alignments
ProfileScan http://myhits.isb-sib.ch/cgi-bin/motif_scan Graphical summary of hits at the amino acid level
ScanProsite http://us.expasy.org/tools/scanprosite/ Graphical summary of hits. Searches only Prosite
Motif Search Tools
Name Website Comments
PATTINPROT http://pbil.ibcp.fr/html/pbil_index.html Scans a protein database for a sequence pattern
SIRW http://sirw.embl.de/index.html Motif search combined with keyword search