copied from Nucleic Acids Research, 2005, Vol. 33, Database issue (link directs to table of contents with many original papers on the below mentioned databases)
back to Database resources and links

No.b Database_name_____ Full_name_and/or_description______________________ URL 3. Protein sequence databases 3.1. General sequence databases 163 EXProt Sequences of proteins with experimentally verified function http://www.cmbi.kun.nl/EXProt/ 542 NCBI Protein database All protein sequences: translated from GenBank and imported from other protein databases http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein 714 PA-GOSUB Protein sequences from model organisms, GO assignment and subcellular localization http://www.cs.ualberta.ca/~bioinfo/PA/ProteomeIndex.html 194 PIR-PSD Protein information resource protein sequence database, has been merged into the UniProt knowledgebase http://pir.georgetown.edu/ 370 PIR-NREF PIR's non-redundant reference protein database http://pir.georgetown.edu/pirwww/pirnref.shtml 565 PRF Protein research foundation database of peptides: sequences, literature and unnatural amino acids http://www.prf.or.jp/en 197 Swiss-Prot Now UniProt/Swiss-Prot: expertly curated protein sequence database, section of the UniProt knowledgebase http://www.expasy.org/sprot 198 TrEMBL Now UniProt/TrEMBL: computer-annotated translations of EMBL nucleotide sequence entries: section of the UniProt knowledgebase http://www.expasy.org/sprot 775 UniParc UniProt archive: a repository of all protein sequences, consisting only of unique identifiers and sequence http://www.uniprot.org/database/archive.shtml 318 UniProt Universal protein knowledgebase: merged data from Swiss-Prot, TrEMBL and PIR protein sequence databases http://www.uniprot.org/ 776 UniRef UniProt non-redundant reference database: clustered sets of related sequences (including splice variants and isoforms) http://www.uniprot.org/database/nref.shtml 3.2. Protein properties 221 AAindex Physicochemical properties of amino acids http://www.genome.ad.jp/aaindex/ 729 ProNIT Thermodynamic data on protein–nucleic acid interactions http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html 280 ProTherm Thermodynamic data for wild-type and mutant proteins http://gibk26.bse.kyutech.ac.jp/jouhou/protherm/protherm.html 772 TECRdb Thermodynamics of enzyme-catalyzed reactions http://xpdb.nist.gov/enzyme_thermodynamics/ 3.3. Protein localization and targeting 444 DBSubLoc Database of protein subcellular localization http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html 375 NESbase Nuclear export signals database http://www.cbs.dtu.dk/databases/NESbase 376 NLSdb Nuclear localization signals http://cubic.bioc.columbia.edu/db/NLSdb/ 704 NMPdb Nuclear matrix associated proteins database http://www.rostlab.org/db/NMPdb/ 706 NOPdb Nucleolar proteome database http://www.lamondlab.com/NOPdb/ 734 PSORTdb Protein subcellular localization in bacteria http://db.psort.org/ 745 SPD Secreted protein database http://spd.cbi.pku.edu.cn 587 THGS Transmembrane helices in genome sequences http://pranag.physics.iisc.ernet.in/thgs/ 589 TMPDB Experimentally characterized transmembrane topologies http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/ 3.4. Protein sequence motifs and active sites 374 ASC Active sequence collection: biologically active peptides http://bioinformatica.isa.cnr.it/ASC/ 203 Blocks Alignments of conserved regions in protein families http://blocks.fhcrc.org/ 440 CSA Catalytic site atlas: active sites and catalytic residues in enzymes of known 3D structure http://www.ebi.ac.uk/thornton-srv/databases/CSA/ 438 COMe Co-ordination of metals etc.: classification of bioinorganic proteins (metalloproteins and some other complex proteins) http://www.ebi.ac.uk/come 771 CopS Comprehensive peptide signature database http://203.195.151.46/copsv2/index.html 666 eBLOCKS Highly conserved protein sequence blocks http://fold.stanford.edu/eblocks/acsearch.html 206 eMOTIF Protein sequence motif determination and searches http://motif.stanford.edu/emotif 179 Metalloprotein Site Database Metal-binding sites in metalloproteins http://metallo.scripps.edu/ 209 O-GlycBase O- and C-linked glycosylation sites in proteins http://www.cbs.dtu.dk/databases/OGLYCBASE/ 717 PDBSite 3D structure of protein functional sites http://srs6.bionet.nsc.ru/srs6/ 187 Phospho.ELM S/T/Y protein phosphorylation sites (formerly PhosphoBase) http://phospho.elm.eu.org/ 193 PROMISE Prosthetic centers and metal ions in protein active sites http://metallo.scripps.edu/PROMISE 215 PROSITE Biologically significant protein patterns and profiles http://www.expasy.org/prosite 732 ProTeus Signature sequences at the protein N- and C-termini http://www.proteus.cs.huji.ac.il/ 3.5. Protein domain databases; protein classification 622 ADDA A database of protein domain classification http://ekhidna.biocenter.helsinki.fi:8080/examples/servlets/adda/ 204 CDD Conserved domain database, includes protein domains from Pfam, SMART, COG and KOG databases http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml 205 CluSTr Clusters of Swiss-Prot TrEMBL proteins http://www.ebi.ac.uk/clustr 671 FunShift Functional divergence between the subfamilies of a protein domain family http://funshift.cgb.ki.se/ 200 Hits A database of protein domains and motifs http://hits.isb-sib.ch/ 207 InterPro Integrated resource of protein families, domains and functional sites http://www.ebi.ac.uk/interpro 208 iProClass Integrated protein classification database http://pir.georgetown.edu/iproclass/ 561 PIRSF Family/superfamily classification of whole proteins http://pir.georgetown.edu/pirsf/ 212 PRINTS Hierarchical gene family fingerprints http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/ 210 Pfam Protein families: multiple sequence alignments and profile hidden Markov models of protein domains http://www.sanger.ac.uk/Software/Pfam/ 727 PRECISE Predicted and consensus interaction sites in enzymes http://precise.bu.edu/precisedb/ 214 ProDom Protein domain families http://www.toulouse.inra.fr/prodom.html 216 ProtoMap Hierarchical classification of Swiss-Prot proteins http://protomap.cornell.edu/ 567 ProtoNet Hierarchical clustering of Swiss-Prot proteins http://www.protonet.cs.huji.ac.il/ 740 S4 Structure-based sequence alignments of SCOP superfamilies http://compbio.mds.qmw.ac.uk/~james/S4.shtml 217 SBASE Protein domain sequences and tools http://www.icgeb.org/sbase 218 SMART Simple modular architecture research tool: signalling, extracellular and chromatin-associated protein domains http://smart.embl-heidelberg.de/ 219 SUPFAM Grouping of sequence families into superfamilies http://pauling.mbu.iisc.ernet.in/~supfam 220 SYSTERS Systematic re-searching and clustering of proteins http://systers.molgen.mpg.de/ 199 TIGRFAMs TIGR protein families adapted for functional annotation http://www.tigr.org/TIGRFAMs 3.6. Databases of individual protein families 156 AARSDB Aminoacyl-tRNA synthetase database http://rose.man.poznan.pl/aars/index.html 308 ASPD Artificial selected proteins/peptides database http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/ 158 BacTregulators Transcriptional regulators of AraC and TetR families http://www.bactregulators.org/ 364 CSDBase Cold shock domain-containing proteins http://www.chemie.uni-marburg.de/~csdbase/ 653 CuticleDB Structural proteins of Arthropod cuticle http://bioinformatics.biol.uoa.gr/cuticleDB 658 DCCP Database of copper-chelating proteins http://sdbi.sdut.edu.cn/DCCP/en/index.php 160 DExH/D Family Database DEAD-box, DEAH-box and DExH-box proteins http://www.helicase.net/dexhd/dbhome.htm 161 Endogenous GPCR List G protein-coupled receptors; expression in cell lines http://www.tumor-gene.org/GPCR/gpcr.html 162 ESTHER Esterases and other alpha/beta hydrolase enzymes http://www.ensam.inra.fr/esther 464 EyeSite Families of proteins functioning in the eye http://eyesite.cryst.bbk.ac.uk/ 166 GPCRDB G protein-coupled receptors database http://www.gpcr.org/7tm/ 679 gpDB G-proteins and their interaction with GPCRs http://bioinformatics.biol.uoa.gr/gpDB 167 Histone Database Histone fold sequences and structures http://research.nhgri.nih.gov/histones/ 169 Homeobox Page Homeobox proteins, classification and evolution http://www.biosci.ki.se/groups/tbu/homeo.html 293 Hox-Pro Homeobox genes database http://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hox-pro00.html 170 Homeodomain Resource Homeodomain sequences, structures and related genetic and genomic information http://research.nhgri.nih.gov/homeodomain/ 366 HORDE Human olfactory receptor data exploratorium http://bioinfo.weizmann.ac.il/HORDE/ 174 InBase Inteins (protein splicing elements) database: properties, sequences, bibliography http://www.neb.com/neb/inteins.html 518 KinG—Kinases in Genomes S/T/Y-specific protein kinases encoded in complete genomes http://hodgkin.mbu.iisc.ernet.in/~king 519 Knottins Database of knottins—small proteins with an unusual ‘disulfide through disulfide’ knot http://knottin.cbs.cnrs.fr 176 LGICdb Ligand-gated ion channel subunit sequences database http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html 368 Lipase Engineering Database Sequence, structure and function of lipases and esterases http://www.led.uni-stuttgart.de/ 524 LOX-DB Mammalian, invertebrate, plant and fungal lipoxygenases http://www.dkfz-heidelberg.de/spec/lox-db/ 177 MEROPS Database of proteolytic enzymes (peptidases) http://merops.sanger.ac.uk/ 369 NPD Nuclear protein database http://npd.hgu.mrc.ac.uk/ 546 NucleaRDB Nuclear receptor superfamily http://www.receptors.org/NR/ 182 Nuclear Receptor Resource Nuclear receptor superfamily http://nrr.georgetown.edu/NRR/nrrhome.htm 183 NUREBASE Nuclear hormone receptors database http://www.ens-lyon.fr/LBMC/laudet/nurebase.html 184 Olfactory Receptor Database Sequences for olfactory receptor-like molecules http://senselab.med.yale.edu/senselab/ordb/ 185 ooTFD Object-oriented transcription factors database http://www.ifti.org/ootfd 188 PKR Protein kinase resource: sequences, enzymology, genetics and molecular and structural properties http://pkr.sdsc.edu/html/index.shtml 759 PLPMDB Pyridoxal-5'-phosphate dependent enzymes mutations http://www.studiofmp.com/plpmdb/ 609 ProLysED A database of bacterial protease systems http://genome.ukm.my/prolyses/ 192 Prolysis Proteases and natural and synthetic protease inhibitors http://delphi.phys.univ-tours.fr/Prolysis/ 224 REBASE Restriction enzymes and associated methylases http://rebase.neb.com/rebase/rebase.html 195 Ribonuclease P Database RNase P sequences, alignments and structures http://www.mbio.ncsu.edu/RNaseP/home.html 573 RPG Ribosomal protein gene database http://ribosome.miyazaki-med.ac.jp/ 575 RTKdb Receptor tyrosine kinase sequences http://pbil.univ-lyon1.fr/RTKdb/ 309 S/MARt dB Nuclear scaffold/matrix attached regions http://smartdb.bioinf.med.uni-goettingen.de/ 741 Scorpion Database of scorpion toxins http://research.i2r.a-star.edu.sg:8080/scorpion/ 372 SDAP Structural database of allergenic proteins and food allergens http://fermi.utmb.edu/SDAP 196 SENTRA Sensory signal transduction proteins http://www-wit.mcs.anl.gov/sentra/ 373 SEVENS 7-transmembrane helix receptors (G-protein-coupled) http://sevens.cbrc.jp/ 248 SRPDB Proteins of the signal recognition particles http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html 314 TrSDB Transcription factor database http://ibb.uab.es/trsdb 399 VKCDB Voltage-gated potassium channel database http://vkcdb.biology.ualberta.ca/ 202 Wnt Database Wnt proteins and phenotypes http://www.stanford.edu/~rnusse/wntwindow.html

^a Each database is shown in the list only once, often in a category that was arbitrarily chosen among two or three appropriate ones. In the online version of this list at the NAR website (http://nar.oupjournals.org/), a database can be listed under two categories.

^b Accession number of the database in the online list; can be used to view the database summary, e.g. http://www3.oup.co.uk/nar/database/summary/1 shows the summary for DDBJ.