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Useful tools and resources for protein family, domain and motif analysis |
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| Database |
Description |
URL |
Published reference |
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| 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] |
Mulder and Apweiler Genome Biology 2001 3:reviews2001.1 doi:10.1186/gb-2001-3-1-reviews2001 |
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