• AAindex -http://www.genome.ad.aj/aaindex/
• AARSDB -http://rose.man.pozman.pl/aars/index.html
• ADDA -http://ekhidna.biocenter.helsinki.fi:8080/examples/servlets/adda/
• ASC -http://bioinformatics.isa.cnr.it/ASC/
• ASPD -http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/
• BacTregulators -http://www.bactregulators.org/
• BIOZON -http://biozon.org
• Blocks -http://blocks.fhcrc.org/
• CDD -http://www.ncbi.nlm.nih.gov/structure/cdd/cdd.shtml
• CluSTr -http://www.ebi.ac.uk/clustr
• COMe -http://www.ebi.ac.uk/come
• CopS -
• CSA -http://www.ebi.ac.uk/thornton-srv/database/CSA
• CSDBase -http://www.chemie.uni-marburg.de/~csdbase/
• CuticleDB -http://bioinformatics.biol.uoa.gr/cuticleDB
• Cybase -http://research.imb.uq.edu.au/cybase/html/index.php
• DBSubLoc -http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html
• DCCP -http://sdbi.sdut.edu.cn/DCCP/en/index.php
• DExH/D Family Database -http://www.helicase.net/dexhd/dbhome.htm
• eBLOCKS -http://fold.stanford.edu/eblocks/acsearch.html
• eMOTIF -http://motif.stanford.edu/emotif
• Endogenous GPCR List -http://www.tumor-gene.org/GPCR/gpcr.html
• EROP-Moscow -http://erop.inbi.ras.ru
• ESTHER -http://www.ensam.inra.fr/esther
• FunShift -http://funshift.cgb.ki.se/
• GPCRDB -http://www.gpcr.org/7tm/
• gpDB -http://bioinformatics.biol.uoa.gr/gpDB
• Histone Database -http://research.nhgri.nih.gov/histones/
• Hits -http://hits.isb-sib.ch/
• Homeobox Page -http://www.biosci.ki.se/groups/tbu/homeo.html
• Homeodomain Resource -http://research.nhgri.nih.gov/homeodomain/
• HORDE -http://bioinfo.weizmann.ac.it/HORDE
• Hox-Pro -http://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hox-pro00.html
• InBase -http://www.neb.com/neb/inteins.html
• InterPro -http://www.ebi.ac.uk/interpro
• iProClass -http://pir.georgetown.edu/gfserver/proclass.html
• iProClass -http://pir.georgetown.edu/iproclass
• KinG – Kinase in Genomes -http://hodkin.mbu.iisc.ernet.in/~king
• Knottins -http://knnottin.cbs.cnrs.fr
• LGICdb -http://www.pasture.fr/recherche/banques/LGIC/LGIC.html
• Lipase Engineering Database -http://www.led.uni-stuttgart.de/
• LOCATE -http://mpdb.imb.uq.edu.au
• LOX-DB -http://www.dkfz-heidelberg.de/spec/lox-db/
• MEROPS -http://merops.sanger.ac.uk/
• Metalloprotein Site -http://metallo.scripps.edu/
• MulPSSM -http://hodgkin.mbu.iisc.ernet.in/~mulpssm
• NESbase -http://www.cbs.dtu.dk/database/NESbase
• NLSdb -http://cubic.bioc.columbia.edu/db/NLSdb/
• NMPdb -http://www.rostlab.org/db/NMPdb/
• NOPdb -http://www.lamondlab.com/NOPdb/
• NPD -http://npd.hgu.mrc.ac.uk/
• Nuclear Receptor Resource -http://nrr.georgetown.edu/NRR/nrrhome.html
• NuclearRDB -http://www.receptors.org/NR/
• NUREBASE -http://www.ens-lyon.fr/LBMC/laudet/nurebase.html
• NURSA -http://www.nursa.org
• O-GlycBase -http://www.cbs.dtu.dk/database/OGLYBASE/
• Olfactory Recptor Database -http://senselab.med.yale.edu/senselab/ordb/
• ooTFD -http://www.ifti.org/ootfd
• PA-GOSUB -http://www.cs.ualberta.ca/~bioinfo/PA/ProteomeIndex.html
• PDBSite -http://srs6.bionet.nsc.ru/srs6/
• Pfam -http://www.sanger.ac.uk/Software/Pfam/
• Phospho.ELM -http://phospho.elm.eu.org/
• PINT -http://pintdb.dyndns.org/index.html
• PIR-ALN-http://pir.gerorgetown.edu/pirwww/dbinfo/piraln.html
• PIR-NREF -http://pir.georgetown.edu/pirwww/pimref.shtml
• PIRSF -http://pir.gerogetown.edu/pirsf/
• PKR -http://pkr.sdsc.edu/html/index.shtml
• PLPMDB -http://www.studiofmp.com/plpmdb/
• PPD -http://www.jenner.ac.uk/ppd
• PRECISE -http://precise.bu.edu/precisedb/
• PRF -http://www.prf.or.jp/en
• PRINTS -http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
• ProDom -http://www.toulouse.inra.fr/prodom.html
• ProLysED -http://genome.ukm.my/prolyses
• Prolysis -http://delphi.phys.univ-tours.fr/Prolysis/
• PROMISE -http://metallo.scripps.edu/PROMISE
• ProNIT -http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html
• ProRule-http://expasy.org/tools/scanprosite
• PROSITE -http://expasy.org/prosite
• ProTeus-http://www.proteus.cs.huji.ac.il/
• ProTherm -http://gibk26.bse.kyutech.ac.jp/jouhou/protherm/protherm.html
• ProtoMap -http://protomap.cornell.edu/
• ProtoNet -http://www.protonet.cs.hugi.ac.il/
• PSORTdb -http://db.psort.org/
• REBASE -http://rebase.neb.com/rebase/rebase.html
• REFOLD -http://www.refold.med.monash.edu.au
• Ribonuclease P Database -http://www.mbio.ncsu.edu/RNaseP/home.html
• RNRdb -http://rnrdb.molbio.su.se/
• RPG -http://ribosome.miyazaki-med.ac.jp/
• RTKdb -http://pbil.univ-lyon1.fr/RTKdb
• S/MARt db -http://smartdb.bioinf.med.uni-goettingen.de/
• S4 -http://compbio.mds.qmw.ac.uk/~james/S4.shtml
• SBASE -http://www.icgeb.org/sbase
• Scorpion -http://research.i2r.a-star.edu.sg:8080/scorpion/
• SDAP -http://fermi.utmb.edu/SDAP
• SENTRA -http://compbio.mcs.anl.gov/sentra/
• SEVENS -http://sevens.cbrc.jp/
• SIMAP -http://mips.gsf.de/services/analysis/simap/
• SitesBase -http://www.bioinformatics.leeds.ac.uk/sb/
• SMART -http://smart.embi-heidelberg.de/
• SPD -http://spd.cbi.pku.edu.cn
• SRPDB -http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html
• SUPFAM -http://pauling.mbu.iisc.ernet.in/~supfam
• Swiss-Prot -http://www.expasy.org/sprot
• SYSTERS -http://systers.molgen.mpg.de/
• TCDB -http://www.tcdb.org/
• TECRdb -http://xpdb.nist.gov/enzyme_thermodynamics/
• THGS -http://pranag.physics.iisc.ernet.in/thgs/
• TIGRFAMs -http://www.tigr.org/TIGRFAMs
• TMPDB -http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB
• TrEMBL -http://www.expasy.org/sprot
• TrSDB -http://bioinf.uab.es/cgi-bin/trsdb/trsdb.pl
• UniParc -http://www.uniprot.org/database/archive.shtml
• UniProt – http://www.uniprot.org/
• UniRef -http://www.uniprot.org/database/nref.shtml
• VKCDB -http://vkcdb.biology.ualberta.ca/
• WntDatabase -http://www.stanford.edu/~musse/wntwindow.html
•EXProt -http://www.cmbi.kun.nl/EXPort/
•MIPS -http://mips.gsf.de/
•NCBI Protein Database -http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein
3D structure of protein funcional sites.
7-transmembrane helix receptors (G-protein coupled).
A database of bacterial protease systems.
A database of protein and gene family classification.
A database of protein domain classification.
A dtabase of protein domains and motifs.
Active Sequence Collection: biologically-active peptides.
Alignments of conserved regions in protein families.
All protein sequences: translated from Genbank and imported from other protein databases.
Aminoacyl-tRNA synthetase database.
Artificial selected proteins/peptides database.
Bioogically significant protein patterns and profiles.
Catalytic Site Atlas: active sites and catalytic residues in enzymes of known 3D structures.
Clustered sets of related sequences from UniProt.
Clusters of Swiss-Prot + TrEMBL proteins.
Cold shock domain-containing proteins.
Comprehensive peptide signature database.
Conserved domain database, includes protein domains from Pfam, SMART, COG and KOG databases.
Coordination of Metals etc.: classification of metalloproteins.
Curated database of protein sequence alignments.
Database of copper-chelating proteins.
Database of individual protein families
Database of Knottins – small proteins with an unusual “disulphide through disulphide” knot..
Database of protein subcelluar localization.
Database of proteolytic enzymes (peptidases).
Database of scorpion toxins.
DEAD-box, DEAH-box and DExH-box proteins.
Endogenous regulatory oligopeptide database.
Estrase and other alpha/beta hydrolase enzmymes.
Experimental data on protein refolding and purification.
Experimentally-charaterized transmembrane topologies.
Family/superfamily classification of whole proteins.
Functional and structural information on PROSITE profiles.
Functional divergence between the subfamilies of a protein domain family.
G protein-coupled receptors database.
G-proteins and their interaction with GPCRs.
Grouping of sequence families into superfamilies.
Hierarchical classification of Swiss-Prot proteins.
Hierarchical clustering of Swiss-Prot proteins.
Hierarchical gene family fingerprints.
Highly conserved protein sequence blocks.
Histone fold sequence and structures.
Homeobox genes database.
Homeobox proteins, classification and evolution.
Homeodomain sequence, structures and related genetic and genomic information.
Human olfactory receptor data exploratorium.
Integrated protein classification database.
Integrated resource of protein families, domains and functional sites.
Inteins (protein splcing elements) database: proteins, sequence, bibliography.
Known ligand binding sites in the PDB.
Ligand-gated ion channel subunit sequences database.
Mammalian, invertebrate, plant and fungal lipoxygenases.
Membarane organization and subcellular localization of mouse proteins..
Metal-binding sites in metalloproteins.
Multiple PSSMs of structural and sequence families.
Now UniProt/SwissProt, part of the UniPort knowledgebase.
Now UniProt/TrEMBL, part of the UniPort knowledgebase.
Nuclear export signal database.
Nuclear hormone receptors database.
Nuclear loalization signals.
Nuclear matrix associated proteins database.
Nuclear protein database.
Nuclear receptor signaling atlas.
Nuclear receptor superfamily.
Nuclear scaffold/matrix attached regions.
Nucleolar protein database.
O- and C- linked glycosylation sites in protein.
Object-oriented transcription factors database.
Physiochemical properties of amino acids.
PIR’s non-redundant reference protein database.
Predicted and consensus interaction sites in enzymes.
Prosthetic centers and metal ions in protein active sites.
Protease and natural and synthetic protease inhibitors.
Protein databases at Munich Information Center for Protein Sequences.
Protein domain database; protein classification
Protein Domain Families.
Protein domain sequence and tools.
Protein families defined by PIR superfamilies and PROSITE patterns.
Protein families: Multiple sequence alignments and profile hidden markov models of protein domains.
Protein localization and targeting
Protein pKa database.
Protein properties
Protein research foundation database of peptides: seuquences, literature and unnatural amino acids.
Protein sequence motif determination and searches.
Protein sequence motifs and active sites
Protein sequences from model organism, GO assignment and subcellular localization.
Protein subcellular localization in bacteria.
Protein-protein interactions thermodynamic database.
Proteins of the signal recognition particles.
Proteins with cyclic backbones.
Prtoein kinase resource: sequence, enzymology, genetics and molecular and structural properties.
Pyridoxal-5′-phosphate dependent enzymes mutation.
Receptor tyrosine kinase sequences.
Restriction enzyme and associated methylases.
Ribonucleotide reductase database.
Ribosomal protein gene database.
RNase P Sequences, alignments and structures.
S/T/Y protein phosphorylation sites(former Phosphobase).
S/T/Y- Specific protein kinase encoded in complete genomes.
Secreted protein database.
Sensory signal transduction proteins.
Sequence, structure and function of lipase and estrases.
Sequences for olfactory receptor-like molecules.
Sequences of proteins with experimentally verified function.
Signature sequences at the protein N- and C- termini..
Similarity Matrix of Proteins: Precomputed similarity data.
Simple Modular Architecture Research Tool: signalling extracelluar and chromatin-associated protein domains.
Structural database of allergenic proteins and food allergens.
Structural proteins of Arthropod cuticle.
Structure-based sequence alignmetns of SCOP superfamilies.
Systematic re-searching and clustreing of proteins.
Thermodynamic data for wild-type and mutant proteins.
Thermodynamic data on protein-nucleic acid interactions.
Thermodynamics of enzyme-catalyzed reactions.
TIGR protein families adapted for functional annotation.
Transcription factor database.
Transcriptional regulators of AraC and TetR families.
Transmembrane helices in genome sequences.
Transporter protein classification database.
UniProt archive, a repository of all protein sequences.
Universal protein knowledgebase.
Voltage-gated potassium channel database.
Wnt proteins and phenotypes.