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Protein Sequence Database

General Sequence Databses

EXProt -http://www.cmbi.kun.nl/EXPort/
Sequences of proteins with experimentally verified function.
MIPS -http://mips.gsf.de/
Protein databases at Munich Information Center for Protein Sequences.
NCBI Protein Database -http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein
All protein sequences: translated from Genbank and imported from other protein databases.
• PA-GOSUB -http://www.cs.ualberta.ca/~bioinfo/PA/ProteomeIndex.html
Protein sequences from model organism, GO assignment and subcellular localization.
• PIR-NREF -http://pir.georgetown.edu/pirwww/pimref.shtml
PIR's non-redundant reference protein database.
• PRF -http://www.prf.or.jp/en
Protein research foundation database of peptides: seuquences, literature and unnatural amino acids.
• Swiss-Prot -
http://www.expasy.org/sprot
Now UniProt/SwissProt, part of the UniPort knowledgebase.
• TCDB -
http://www.tcdb.org/
Transporter protein classification database.
• TrEMBL -
http://www.expasy.org/sprot
Now UniProt/TrEMBL, part of the UniPort knowledgebase.
• UniParc -
http://www.uniprot.org/database/archive.shtml
UniProt archive, a repository of all protein sequences.
• UniProt - http://www.uniprot.org/
Universal protein knowledgebase.
• UniRef -
http://www.uniprot.org/database/nref.shtml
Clustered sets of related sequences from UniProt.

Protein properties

• AAindex -http://www.genome.ad.aj/aaindex/
Physiochemical properties of amino acids.
• Cybase -
http://research.imb.uq.edu.au/cybase/html/index.php
Proteins with cyclic backbones.
• PINT -
http://pintdb.dyndns.org/index.html
Protein-protein interactions thermodynamic database.
• PPD -
http://www.jenner.ac.uk/ppd
Protein pKa database.
• ProNIT -
http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html
Thermodynamic data on protein-nucleic acid interactions.
• ProTherm -
http://gibk26.bse.kyutech.ac.jp/jouhou/protherm/protherm.html
Thermodynamic data for wild-type and mutant proteins.
• REFOLD -
http://www.refold.med.monash.edu.au
Experimental data on protein refolding and purification.
• TECRdb -
http://xpdb.nist.gov/enzyme_thermodynamics/
Thermodynamics of enzyme-catalyzed reactions.

Protein localization and targeting

• DBSubLoc -http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html
Database of protein subcelluar localization.
• LOCATE -
http://mpdb.imb.uq.edu.au
Membarane organization and subcellular localization of mouse proteins..
• NESbase -
http://www.cbs.dtu.dk/database/NESbase
Nuclear export signal database.
• NLSdb -http://cubic.bioc.columbia.edu/db/NLSdb/
Nuclear loalization signals.
• NMPdb -http://www.rostlab.org/db/NMPdb/
Nuclear matrix associated proteins database.
• NOPdb -http://www.lamondlab.com/NOPdb/
Nucleolar protein database.
• NURSA -http://www.nursa.org
Nuclear receptor signaling atlas.
• PSORTdb -http://db.psort.org/
Protein subcellular localization in bacteria.
• SPD -http://spd.cbi.pku.edu.cn
Secreted protein database.
• THGS -
http://pranag.physics.iisc.ernet.in/thgs/
Transmembrane helices in genome sequences.
• TMPDB -http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB
Experimentally-charaterized transmembrane topologies.

Protein sequence motifs and active sites

• ASC -http://bioinformatics.isa.cnr.it/ASC/
Active Sequence Collection: biologically-active peptides.
• Blocks -
http://blocks.fhcrc.org/
Alignments of conserved regions in protein families.
• CSA -
http://www.ebi.ac.uk/thornton-srv/database/CSA
Catalytic Site Atlas: active sites and catalytic residues in enzymes of known 3D structures.
• COMe -http://www.ebi.ac.uk/come
Coordination of Metals etc.: classification of metalloproteins.
• CopS -http://203.90.127.70/copsv2/index.html
Comprehensive peptide signature database.
• eBLOCKS -http://fold.stanford.edu/eblocks/acsearch.html
Highly conserved protein sequence blocks.
• eMOTIF -
http://motif.stanford.edu/emotif
Protein sequence motif determination and searches.
• Metalloprotein Site -http://metallo.scripps.edu/
Metal-binding sites in metalloproteins.
• O-GlycBase -
http://www.cbs.dtu.dk/database/OGLYBASE/
O- and C- linked glycosylation sites in protein.
• PDBSite -http://srs6.bionet.nsc.ru/srs6/
3D structure of protein funcional sites.
• Phospho.ELM -http://phospho.elm.eu.org/
S/T/Y protein phosphorylation sites(former Phosphobase).
• PROMISE -http://metallo.scripps.edu/PROMISE
Prosthetic centers and metal ions in protein active sites.
• ProRule-
http://expasy.org/tools/scanprosite
Functional and structural information on PROSITE profiles.
• PROSITE -
http://expasy.org/prosite
Bioogically significant protein patterns and profiles.
• ProTeus-
http://www.proteus.cs.huji.ac.il/
Signature sequences at the protein N- and C- termini..
• SitesBase -http://www.bioinformatics.leeds.ac.uk/sb/
Known ligand binding sites in the PDB.

Protein domain database; protein classification

• ADDA -http://ekhidna.biocenter.helsinki.fi:8080/examples/servlets/adda/
A database of protein domain classification.
• BIOZON -
http://biozon.org
A database of protein and gene family classification.
• CDD -
http://www.ncbi.nlm.nih.gov/structure/cdd/cdd.shtml
Conserved domain database, includes protein domains from Pfam, SMART, COG and KOG databases.
• CluSTr -http://www.ebi.ac.uk/clustr
Clusters of Swiss-Prot + TrEMBL proteins.
• FunShift -http://funshift.cgb.ki.se/
Functional divergence between the subfamilies of a protein domain family.
• Hits -http://hits.isb-sib.ch/
A dtabase of protein domains and motifs.
• InterPro -
http://www.ebi.ac.uk/interpro
Integrated resource of protein families, domains and functional sites.
• iProClass -http://pir.georgetown.edu/iproclass
Integrated protein classification database.
• MulPSSM -
http://hodgkin.mbu.iisc.ernet.in/~mulpssm
Multiple PSSMs of structural and sequence families.
• PIRSF -http://pir.gerogetown.edu/pirsf/
Family/superfamily classification of whole proteins.
• PRINTS -http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
Hierarchical gene family fingerprints.
• Pfam -http://www.sanger.ac.uk/Software/Pfam/
Protein families: Multiple sequence alignments and profile hidden markov models of protein domains.
• PIR-ALN-
http://pir.gerorgetown.edu/pirwww/dbinfo/piraln.html
Curated database of protein sequence alignments.
• PRECISE -
http://precise.bu.edu/precisedb/
Predicted and consensus interaction sites in enzymes.
• iProClass -
http://pir.georgetown.edu/gfserver/proclass.html
Protein families defined by PIR superfamilies and PROSITE patterns.
• ProDom -
http://www.toulouse.inra.fr/prodom.html
Protein Domain Families.
• ProtoMap -
http://protomap.cornell.edu/
Hierarchical classification of Swiss-Prot proteins.
• ProtoNet -
http://www.protonet.cs.hugi.ac.il/
Hierarchical clustering of Swiss-Prot proteins.
• S4 -http://compbio.mds.qmw.ac.uk/~james/S4.shtml
Structure-based sequence alignmetns of SCOP superfamilies.
• SBASE -http://www.icgeb.org/sbase
Protein domain sequence and tools.
• SIMAP -http://mips.gsf.de/services/analysis/simap/
Similarity Matrix of Proteins: Precomputed similarity data.
• SMART -
http://smart.embi-heidelberg.de/
Simple Modular Architecture Research Tool: signalling extracelluar and chromatin-associated protein domains.
• SUPFAM -
http://pauling.mbu.iisc.ernet.in/~supfam
Grouping of sequence families into superfamilies.
• SYSTERS -
http://systers.molgen.mpg.de/
Systematic re-searching and clustreing of proteins.
• TIGRFAMs -
http://www.tigr.org/TIGRFAMs
TIGR protein families adapted for functional annotation.

Database of individual protein families

• AARSDB -http://rose.man.pozman.pl/aars/index.html
Aminoacyl-tRNA synthetase database.
• ASPD -
http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/
Artificial selected proteins/peptides database.
• BacTregulators -
http://www.bactregulators.org/
Transcriptional regulators of AraC and TetR families.
• CSDBase -http://www.chemie.uni-marburg.de/~csdbase/
Cold shock domain-containing proteins.
• CuticleDB -http://bioinformatics.biol.uoa.gr/cuticleDB
Structural proteins of Arthropod cuticle.
• DCCP -http://sdbi.sdut.edu.cn/DCCP/en/index.php
Database of copper-chelating proteins.
• DExH/D Family Database -
http://www.helicase.net/dexhd/dbhome.htm
DEAD-box, DEAH-box and DExH-box proteins.
• Endogenous GPCR List -http://www.tumor-gene.org/GPCR/gpcr.html
G protein-coupled receptors database.
• EROP-Moscow -
http://erop.inbi.ras.ru
Endogenous regulatory oligopeptide database.
• ESTHER -http://www.ensam.inra.fr/esther
Estrase and other alpha/beta hydrolase enzmymes.
• GPCRDB -http://www.gpcr.org/7tm/
G protein-coupled receptors database.
• gpDB -http://bioinformatics.biol.uoa.gr/gpDB
G-proteins and their interaction with GPCRs.
• Histone Database -
http://research.nhgri.nih.gov/histones/
Histone fold sequence and structures.
• Homeobox Page -
http://www.biosci.ki.se/groups/tbu/homeo.html
Homeobox proteins, classification and evolution.
• Hox-Pro -
http://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hox-pro00.html
Homeobox genes database.
• Homeodomain Resource -
http://research.nhgri.nih.gov/homeodomain/
Homeodomain sequence, structures and related genetic and genomic information.
• HORDE -
http://bioinfo.weizmann.ac.it/HORDE
Human olfactory receptor data exploratorium.
• InBase -
http://www.neb.com/neb/inteins.html
Inteins (protein splcing elements) database: proteins, sequence, bibliography.
• KinG - Kinase in Genomes -http://hodkin.mbu.iisc.ernet.in/~king
S/T/Y- Specific protein kinase encoded in complete genomes.
• Knottins -http://knnottin.cbs.cnrs.fr
Database of Knottins - small proteins with an unusual "disulphide through disulphide" knot..
• LGICdb -http://www.pasture.fr/recherche/banques/LGIC/LGIC.html
Ligand-gated ion channel subunit sequences database.
• Lipase Engineering Database -
http://www.led.uni-stuttgart.de/
Sequence, structure and function of lipase and estrases.
• LOX-DB -
http://www.dkfz-heidelberg.de/spec/lox-db/
Mammalian, invertebrate, plant and fungal lipoxygenases.
• MEROPS -
http://merops.sanger.ac.uk/
Database of proteolytic enzymes (peptidases).
• NPD -
http://npd.hgu.mrc.ac.uk/
Nuclear protein database.
• NuclearRDB -
http://www.receptors.org/NR/
Nuclear receptor superfamily.
• Nuclear Receptor Resource -
http://nrr.georgetown.edu/NRR/nrrhome.html
Nuclear receptor superfamily.
• NUREBASE -
http://www.ens-lyon.fr/LBMC/laudet/nurebase.html
Nuclear hormone receptors database.
• Olfactory Recptor Database -http://senselab.med.yale.edu/senselab/ordb/
Sequences for olfactory receptor-like molecules.
• ooTFD -http://www.ifti.org/ootfd
Object-oriented transcription factors database.
• PKR -http://pkr.sdsc.edu/html/index.shtml
Prtoein kinase resource: sequence, enzymology, genetics and molecular and structural properties.
• PLPMDB -
http://www.studiofmp.com/plpmdb/
Pyridoxal-5'-phosphate dependent enzymes mutation.
• ProLysED -http://genome.ukm.my/prolyses
A database of bacterial protease systems.
• Prolysis -
http://delphi.phys.univ-tours.fr/Prolysis/
Protease and natural and synthetic protease inhibitors.
• REBASE -http://rebase.neb.com/rebase/rebase.html
Restriction enzyme and associated methylases.
• Ribonuclease P Database -http://www.mbio.ncsu.edu/RNaseP/home.html
RNase P Sequences, alignments and structures.
• RPG -http://ribosome.miyazaki-med.ac.jp/
Ribosomal protein gene database.
• RTKdb -
http://pbil.univ-lyon1.fr/RTKdb
Receptor tyrosine kinase sequences.
• RNRdb -
http://rnrdb.molbio.su.se/
Ribonucleotide reductase database.
• S/MARt db -
http://smartdb.bioinf.med.uni-goettingen.de/
Nuclear scaffold/matrix attached regions.
• Scorpion -
http://research.i2r.a-star.edu.sg:8080/scorpion/
Database of scorpion toxins.
• SDAP -
http://fermi.utmb.edu/SDAP
Structural database of allergenic proteins and food allergens.
• SENTRA -
http://compbio.mcs.anl.gov/sentra/
Sensory signal transduction proteins.
• SEVENS -http://sevens.cbrc.jp/
7-transmembrane helix receptors (G-protein coupled).
• SRPDB -http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html
Proteins of the signal recognition particles.
• TrSDB -http://bioinf.uab.es/cgi-bin/trsdb/trsdb.pl
Transcription factor database.
• VKCDB -
http://vkcdb.biology.ualberta.ca/
Voltage-gated potassium channel database.
• WntDatabase -
http://www.stanford.edu/~musse/wntwindow.html
Wnt proteins and phenotypes.