[转载]蛋白质序列数据库

3. Protein Sequence Databases
3.1. General sequence databases
EXProt	Sequences of proteins with experimentally verified function	http://wwwNaNbi.kun.nl/EXProt/
MIPS resources	Munich Information Center for Protein Sequences databases	http://mips.gsf.de/
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
PA-GOSUB	Protein sequences from model organisms, GO assignment and subcellular localization	http://www.cs.ualberta.ca/~bioinfo/PA/
PIR	Protein Information Resource	http://pir.georgetown.edu
PRF	Protein research foundation database of peptides	http://www.prf.or.jp/en/index.shtml
TCDB	Transporter protein classification database	http://www.tcdb.org/
UniParc	UniProt archive, a repository of all protein sequences	http://www.uniprot.org/database/archive.shtml
UniProt	Universal Protein knowledgebase, combined information from Swiss-Prot, TrEMBL, and PIR	http://www.uniprot.org
UniProtKB\Swiss-Prot	Formerly SwissProt, part of the UniProt knowledgebase	http://www.expasy.org/sprot
UniProtKB\TrEMBL	Now UniProt/TrEMBL, part of the UniProt knowledgebase	http://www.uniprot.org/database/knowledgebase.shtml
UniRef	Clustered sets of related sequences from UniProt	http://www.uniprot.org/database/nref.shtml
UniSave	UniProtKB Sequence/Annotation Version Archive	http://www.ebi.ac.uk/uniprot/unisave/
3.2. Protein properties
AAindex	Physicochemical properties of amino acids	http://www.genome.ad.jp/aaindex/
BindingDB	Binding affinities of protein-ligand and other complexes	http://www.bindingdb.org/bind/index.jsp
CyBase	Proteins with cyclic backbones	http://research1t.imb.uq.edu.au/cybase
dbPTM	Information on post-translational modification of proteins	http://dbptm.mbc.nctu.edu.tw/
iProLINK	Annotated literature sources for protein features and names	http://pir.georgetown.edu/iprolink
MALISAM	Manual alignments for structurally analogous motifs in proteins	http://prodata.swmed.edu/malisam
MegaMotifbase	Structural motifs in protein families and superfamilies	http://caps.ncbs.res.in/MegaMotifbase/index.html
PIDD	Protein inter-atomic distances database	http://pidd.math.iastate.edu
PINT	Protein-protein interactions thermodynamic database	http://pintdb.dyndns.org/index.html
PPD	Experimentally-determined protein pKa values	http://www.jenner.ac.uk/ppd/
PPT-DB	Protein Property Prediction and Testing Database	http://redpoll.pharmacy.ualberta.ca/PPT_DB/public_html/PPT_main.html
ProTherm	Thermodynamic data for wild-type and mutant proteins	http://gibk26.bse.kyutech.ac.jp/jouhou/protherm/protherm.html
PRTAD	Protein residue torsion angle database	http://www.math.iastate.edu/prtad
REFOLD	Experimental data on protein refolding and purification	http://refold.med.monash.edu.au
3.3. Protein localization and targeting
DBSubLoc -	Database of protein Subcellular Localization	http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html
eSLDB	eukaryotic proteins Subcellular Localization Database	http://gpcr.biocomp.unibo.it/esldb
InterFil	Human Intermediate Filament database	http://www.interfil.org
LOCATE	Subcellular localization of mouse proteins	http://locate.imb.uq.edu.au/
MiCroKit	Midbody, Centrosome and Kinetochore proteins	http://bioinformatics.lcd-ustc.org/microkit/
MitoDrome	Nuclear-encoded mitochondrial proteins of Drosophila	http://www2.ba.itb.cnr.it/MitoDrome/
MitoRes	Nuclear genes coding for mitochondrial proteins	http://www2.ba.itb.cnr.it/MitoNuc/
NESbase	Nuclear export signals database	http://www.cbs.dtu.dk/databases/NESbase
NLSdb	Nuclear localization signals	http://cubic.bioc.columbia.edu/db/NLSdb/
NMPdb	Nuclear matrix associated proteins database	http://www.rostlab.org/db/NMPdb/
NOPdb:	Nucleolar proteome database	http://www.lamondlab.com/NOPdb/
NPD	Nuclear Protein Database	http://npd.hgu.mrc.ac.uk
Nuclear Receptor Resource	Nuclear receptor superfamily	http://nrr.georgetown.edu/NRR/nrrhome.htm
NUREBASE	Nuclear hormone receptors database	http://www.ens-lyon.fr/LBMC/laudet/nurebase/nurebase.html
NURSA	Nuclear receptor signaling atlas	http://www.nursa.org
PSORTdb	Protein subcellular localization in bacteria	http://db.psort.org/
Secreted Protein DB	Secreted proteins from human, mouse and rat	http://spd.cbi.pku.edu.cn
SUBA	Subcellular localisation of Arabidopsis proteins	http://www.suba.bcs.uwa.edu.au/
THGS	Transmembrane Helices in Genome Sequences	http://pranag.physics.iisc.ernet.in/thgs/
TopDB	Topology Data Bank of transmembrane proteins	http://topdb.enzim.hu
Transmembrane Protein Database	Transmembrane proteins with experimentally-characterized transmembrane topologies	http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/
3.4. Protein sequence motifs and active sites
ASC	Active Sequence Collection	http://bioinformatica.isa.cnr.it/ASC/
Blocks	Alignments of conserved regions in protein families	http://blocks.fhcrc.org
COMe	Co-Ordination of Metals etc.	http://www.ebi.ac.uk/come/
CoPS	Comprehensive peptide signature database	http://cops.igib.res.in/copsv2/index.html
CSA	Catalytic Site Atlas	http://www.ebi.ac.uk/thornton-srv/databases/CSA/
eBLOCKS	Highly conserved protein sequence blocks	http://fold.stanford.edu/eblocks/acsearch.html
eF-site	Electrostatic surface of Functional site	http://ef-site.protein.osaka-u.ac.jp/eF-site
eMOTIF	Protein sequence motif determination and searches	http://motif.stanford.edu/emotif
FireDB	Functionally important residues in protein structures	http://firedb.bioinfo.cnio.es/
InterPro	Integrated resource of protein families, domains and functional sites	http://www.ebi.ac.uk/interpro
Metalloprotein Site DB	Metal-binding sites in metalloproteins	http://metallo.scripps.edu/
O-GLYCBASE	O- and C-linked glycosylation sites in proteins	http://www.cbs.dtu.dk/databases/OGLYCBASE/
PDBSite	3D structure of protein functional sites	http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?-page+LibInfo+-newId+-lib+PDBSite
Phospho.ELM	S/T/Y protein phosphorylation sites (former PhosphoBase)	http://phospho.elm.eu.org/
Phospho3D	3D structures of protein phosphorylation sites	http://cbm.bio.uniroma2.it/p3d/
PRINTS	Hierarchical gene family fingerprints	http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
PROMISE	Prosthetic centers and metal ions in protein active sites	http://metallo.scripps.edu/PROMISE/
ProRule	Functional and structural information on PROSITE profiles	http://www.expasy.org/prosite/prorule.html
PROSITE	Biologically-significant protein patterns and profiles	http://www.expasy.org/prosite
ProTeus	Signature sequences at the protein N- and C-termini	http://www.proteus.cs.huji.ac.il
SitesBase	Known ligand binding sites in the PDB	http://www.modelling.leeds.ac.uk/sb/
3.5. Protein domain databases; protein classification
ADDA	Database of protein domain classification	http://ekhidna.biocenter.helsinki.fi/sqgraph/pairsdb
BAliBASE	Benchmark database for comparison of multiple sequence alignments	http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html
Benchmark	Protein classification benchmark collection: training/test sets for machine learning	http://net.icgeb.org/benchmark/
BIOZON	Database of gene and protein familiy classification	http://biozon.org
CDD	Conserved domain database, includes protein domains from Pfam, SMART, COG and KOG databases	http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
CluSTr	Clusters of UniProt Knowledgebase and IPI proteins	http://www.ebi.ac.uk/clustr/
COG	Clusters of orthologous groups of proteins	http://www.ncbi.nlm.nih.gov/COG
DomIns	Database of Domain Insertions	http://www.domins.org/
eggNOG	Evolutionary genealogy of genes: Non-supervised Orthologous Groups	http://eggnog.embl.de
EPGD	Eukaryotic Paralog Group Database	http://epgd.biosino.org:8080/EPGD/
EVEREST	Automatically generated protein domain families	http://www.everest.cs.huji.ac.il
FunShift	Functional divergence between the subfamilies of a protein domain family	http://FunShift.cgb.ki.se
FusionDB	Database of bacterial and archaeal gene fusion events	http://www.igs.cnrs-mrs.fr/FusionDB/
Hits	Database of protein domains and motifs	http://hits.isb-sib.ch
HSSP	Homology-derived structures of proteins	http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+HSSP
InterDom	Putative protein domain interactions	http://interdom.i2r.a-star.edu.sg/
iProClass	Integrated protein classification database	http://pir.georgetown.edu/iproclass/
MulPSSM	Multiple PSSMs of structural and sequence families	http://hodgkin.mbu.iisc.ernet.in/~mulpssm
PairsDB	Pairwise alignments of all sequences in UniProt	http://pairsdb.csc.fi
PALI	Phylogeny and alignment of homologous protein structures	http://pauling.mbu.iisc.ernet.in/~pali
PANTHER	Protein sequence evolution mapped to functions and pathways	http://www.pantherdb.org
Pfam	Protein families: Multiple sequence alignments and profile hidden Markov models of protein domains	http://pfam.sanger.ac.uk/
PhyloFacts	Phylogenomic analysis of protein families	http://phylogenomics.berkeley.edu/phylofacts/
PIRSF	Family/superfamily classification of whole proteins	http://pir.georgetown.edu/pirsf/
ProDom	Protein domain families	http://prodom.prabi.fr/
ProtoMap	Hierarchical classification of Swiss-Prot proteins	http://protomap.cornell.edu
ProtoNet	Hierarchical clustering of Swiss-Prot proteins	http://www.protonet.cs.huji.ac.il/
SBASE	Protein domain sequences and tools	http://www.icgeb.org/sbase
SIMAP	Similarity matrix of proteins: precomputed similarity data	http://mips.gsf.de/simap/
SISYPHUS	Structural alignments for proteins with non-trivial relationships	http://sisyphus.mrc-cpe.cam.ac.uk
SMART	Simple modular architecture research tool: signalling, extracellular and chromatin-associated protein domains	http://smart.embl-heidelberg.de
SUPFAM	Grouping of sequence families into superfamilies	http://pauling.mbu.iisc.ernet.in/~supfam
TIGRFAMs	TIGR protein families adapted for functional annotation	http://www.tigr.org/TIGRFAMs
3.6. Databases of individual protein families
ABCdb	Archaeal and bacterial ABC transporter database	http://www-abcdb.biotoul.fr
Aminoacyl-tRNA synthetases database	Aminoacyl-tRNA synthetase database	http://rose.man.poznan.pl/aars/index.html
Animal Toxin DB	Database of animal toxins	http://protchem.hunnu.edu.cn/toxin
ARAMEMNON	Arabidopsis thaliana membrane proteins and transporters	http://aramemnon.botanik.uni-koeln.de
BACTIBASE	Database of bacteriocin natural antimicrobial peptides	http://www.pfba-lab.org/bactibase
BacTregulators	Transcriptional regulators of AraC and TetR families	No longer maintained
BANMOKI	Database of bacterial nucleoside monophosphate kinases	http://www.ces.clemson.edu/compbio/databases/kinases
ChromDB	Chromatin-associated proteins in a broad range of organisms	http://www.chromdb.org
cpnDB	Chaperonin database	http://cpndb.cbr.nrc.ca/
CREMOFAC	Database of chromatin remodeling factors	http://www.jncasr.ac.in/cremofac/
CSDBase	Cold Shock Domain database	http://www.chemie.uni-marburg.de/~csdbase/
CyMoBase	Cytoskeletal and motor proteins database	http://www.motorprotein.de/cymobase
DB-PABP	Experimentally characterized polyanion-binding proteins	http://ppa.bcf.ku.edu/DB_PABP/
DCCP	Database of Copper-Chelating Proteins	http://sdbi.sdut.edu.cn/DCCP/en/index.php
Defensins Knowledgebase	Antimicrobial peptides of the defensin family	http://defensins.bii.a-star.edu.sg/
DExH/D Family DB	DEAD-box, DEAH-box and DExH-box proteins	http://www.helicase.net/dexhd/dbhome.htm
DSD	Database of dehydrogenase stereospecificities	http://www.jenner.ac.uk/DSD
Endogenous GPCR List	G protein-coupled receptors; expression in cell lines	http://www.tumor-gene.org/GPCR/gpcr.html
EROP-Moscow	Database of Endogenous Regulatory OligoPeptides	http://erop.inbi.ras.ru
ESTHER	Esterases and other alpha/beta hydrolase enzymes	http://bioweb.ensam.inra.fr/ESTHER/general?what=index
FUNPEP	Low-complexity peptides capable of forming amyloid plaque	http://wwwNaNbi.kun.nl/swift/FUNPEP/gergo/
GPCRDB	G protein-coupled receptors database	http://www.gpcr.org/7tm/
gpDB	G-protein database: G-proteins and their interaction with GPCRs	http://bioinformatics.biol.uoa.gr/gpDB
Heme Protein DB	Heme protein structure, heme type, axial ligands, and heme protein reduction potential (Em) values	http://heme.chem.columbia.edu/heme.php
Histone Database	Histone fold sequences and structures	http://research.nhgri.nih.gov/histones/
HIV RT and Protease Sequence Database	HIV reverse transcriptase and protease sequences	http://hivdb.stanford.edu
Homeobox Page	Homeobox proteins, classification, and evolution	http://www.biosci.ki.se/groups/tbu/homeo.html
Homeodomain Resource	Homeodomain sequences, structures, and related genetic and genomic information	http://research.nhgri.nih.gov/homeodomain/
InBase	Inteins (protein splicing elements) database: properties, sequences, bibliography	http://www.neb.com/neb/inteins.html
KinG	Kinases in Genomes: Ser/Thr/Tyr kinases encoded in the completely sequenced genomes	http://hodgkin.mbu.iisc.ernet.in/~king
Knottin database	Database of knottins, small proteins with an unusual "disulfide through disulfide" knot	http://knottin.cbs.cnrs.fr/
LGICdb	Ligand-gated ion channel subunit sequences database	http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html
Lipase Engineering DB	Sequence, structure and function of lipases and esterases	http://www.led.uni-stuttgart.de/
LOX-DB	Mammalian, invertebrate, plant and fungal lipoxygenases	http://www.dkfz-heidelberg.de/spec/lox-db/
MEROPS	Database of proteolytic enzymes (peptidases)	http://merops.sanger.ac.uk/
NORINE	Database of nonribosomal peptides	http://bioinfo.lifl.fr/norine/
NucleaRDB	Nuclear receptor superfamily	http://www.receptors.org/NR/
Olfactory Receptor DB	Sequences for olfactory receptor-like molecules	http://senselab.med.yale.edu/senselab/ordb/
Peptaibol	Peptaibol (antibiotic peptide) sequences	http://www.cryst.bbk.ac.uk/peptaibol/
PhytoProt	Clusters of (predicted) plant proteins	http://urgi.versailles.inra.fr/phytoprot/
PLANT-PIs	Plant protease inhibitors	http://bighost.area.ba.cnr.it/PLANT-Pis
PlantsP/PlantsT	Plant proteins involved in phosphorylation and transport	http://plantsp.sdsc.edu
PLPMDB	Pyridoxal-5'-phosphate dependent enzymes mutations	http://www.studiofmp.com/plpmdb/
ProLysED	Database of bacterial protease systems	http://genome.ukm.my/prolyses/
Prolysis	Proteases and natural and synthetic protease inhibitors	http://delphi.phys.univ-tours.fr/Prolysis/
Protein kinase resource	Protein kinase resource: sequences, enzymology, genetics and molecular and structural properties	http://www.kinasenet.org/pkr/
REBASE	Restriction enzymes and associated methylases	http://rebase.neb.com/rebase/rebase.html
RNAse P Database	Ribonuclease P sequences, alignments and structures	http://www.mbio.ncsu.edu/RNaseP/home.html
RNRdb	Ribonucleotide reductase database	http://rnrdb.molbio.su.se/
RPG	Ribosomal Protein Gene database	http://ribosome.miyazaki-med.ac.jp/
RTKdb	Receptor Tyrosine Kinase database	http://pbil.univ-lyon1.fr/RTKdb/
SDAP	Structural database of allergenic proteins and food allergens	http://fermi.utmb.edu/SDAP
SelenoDB	Database of selenoprotein genes, proteins and SECIS elements	http://www.selenodb.org/
SENTRA	Sensory signal transduction proteins	http://compbio.mcs.anl.gov/sentra/
SEVENS	7-transmembrane helix receptors (G-protein-coupled)	http://sevens.cbrc.jp/1.20/
Telomerase database	Sequences and structures of the RNA and protein subunits of telomerase, mutations of telomerase components	http://telomerase.asu.edu
TransportDB	Predicted membrane transporters in complete genomes, classified according to the TC classification system	http://www.membranetransport.org
VKCDB	Voltage-gated K+ Channel Database	http://vkcdb.biology.ualberta.ca/
Wnt Database	Wnt proteins and phenotypes	http://www.stanford.edu/~rnusse/wntwindow.html

 

本文引用地址：http://blog.sciencenet.cn/blog-748683-886125.html  此文来自科学网潘兴亮博客，转载请注明出处。