| Nob |
Database name |
Full name and/or description |
URL |
| 1. Nucleotide Sequence Databases |
| 1.1. International Nucleotide Sequence Database Collaboration |
| 1 |
DDBJ - DNA Data Bank of Japan |
All known nucleotide and protein sequences |
http://www.ddbj.nig.ac.jp | |
| 2 |
EMBL Nucleotide Sequence Database |
All known nucleotide and protein sequences |
http://www.ebi.ac.uk/embl.html | |
| 3 |
GenBank® |
All known nucleotide and protein sequences |
http://www.ncbi.nlm.nih.gov/Entrez | |
| 1.2. Coding and coding DNA: genes, motifs and regulatory sites |
| 403 |
ACLAME |
A classification of genetic mobile elements |
http://aclame.ulb.ac.be/ | |
| 337 |
CORG |
Comparative Regulatory Genomics: conserved non-coding blocks in vertebrate species |
http://corg.molgen.mpg.de | |
| 30 |
CUTG |
Codon Usage Tabulated from GenBank |
http://www.kazusa.or.jp/codon/ | |
| 1157 |
ECRbase |
Database of Evolutionary Conserved Regions, promoters, and transcription factor binding sites |
http://ecrbase.dcode.org/ | |
| 668 |
Entrez Gene |
Gene-centered information at NCBI |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene | |
| 669 |
FESD |
Functional Element SNPs Database: SNPs located within promoters, UTRs, etc., of human genes |
http://sysbio.kribb.re.kr/FESD/ | |
| 468 |
FREP |
Functional Repeats in mouse cDNAs |
http://facts.gsc.riken.go.jp/FREP/ | |
| 480 |
Genetic Codes |
Genetic codes in various organisms and organelles |
http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c | |
| 1079 |
GISSD |
Group I Intron Sequence and Structure Database |
http://www.rna.whu.edu.cn/gissd | |
| 1083 |
GyDB |
Gypsy database of mobile genetic elements |
http://gydb.uv.es/gydb/intro.htm | |
| 825 |
HumHot |
Human meiotic recombination hot spots |
http://www.jncasr.ac.in/humhot/ | |
| 932 |
InSatDb |
Sequences and properties of insect microsatellites |
http://www.cdfd.org.in/insatdb | |
| 832 |
ISfinder |
Insertion sequences from bacteria and archaea |
http://www-is.biotoul.fr | |
| 512 |
Islander |
Pathogenicity islands and prophages in bacterial genomes |
http://www.indiana.edu/~islander | |
| 697 |
L1Base |
Functional annotation and prediction of LINE-1 elements |
http://line1.molgen.mpg.de | |
| 19 |
MethDB |
DNA methylation data, patterns and profiles |
http://www.methdb.de | |
| 343 |
MICdb |
Prokaryotic microsatellites |
http://210.212.212.7/MIC/index.html | |
| 707 |
NPRD |
Nucleosome Positioning Region Database |
http://srs6.bionet.nsc.ru/srs6bin/cgi-bin/wgetz?page+ LibInfo+-id+2Xnp11RCiPU+-lib+NUCLEOSOME | |
| 931 |
OriDB |
DNA Replication Origin Database: Confirmed and predicted sites |
http://www.oridb.org/ | |
| 551 |
PACRAT |
Archaeal and bacterial intergenic sequence features |
No longer maintained |
| 608 |
PANDIT |
Protein and associated nucleotide domains with inferred trees |
http://www.ebi.ac.uk/goldman-srv/pandit/ | |
| 933 |
Patome |
Annotated sequences from patents and patent applications |
http://www.patome.org | |
| 958 |
PolymiRTS |
Polymorphism in microRNA Target Site |
http://compbio.utmem.edu/miRSNP/ | |
| 1007 |
PseudoGene.org |
Pseudogenes in eukaryotic and prokaryotic genomes |
http://www.pseudogene.org/ | |
| 21 |
RECODE |
Genes using programmed translational recoding in their expression |
http://recode.genetics.utah.edu | |
| 391 |
RefSeq |
Reference Sequence database: an integrated, non-redundant set of genomic DNA, RNA, and protein sequences |
http://www.ncbi.nlm.nih.gov/RefSeq/ | |
| 1019 |
RetrOryza |
LTR-retrotransposons in rice |
http://www.retroryza.org | |
| 309 |
S/MARt DB |
Nuclear scaffold/matrix attached regions |
http://smartdb.bioinf.med.uni-goettingen.de/ | |
| 1013 |
SNPSTR |
Microsatellite compound markers in 5 vertebrate genomes |
http://www3.imperial.ac.uk/theoreticalgenomics/data-software | |
| 47 |
STRBase |
Short tandem DNA repeats database |
http://www.cstl.nist.gov/div831/strbase/ | |
| 929 |
Synthetic Gene DB |
Synthetic genes described in peer-reviewed literature |
http://www.evolvingcode.net/codon/sgdb/index.php | |
| 588 |
TIGR plant repeat DB |
Classification of repetitive sequences in plant genomes |
http://www.tigr.org/tdb/e2k1/plant.repeats | |
| 1141 |
TranspoGene |
Transposed elements influence on the transcriptome of seven vertebrates and invertebrates |
http://transpogene.tau.ac.il/ | |
| 1035 |
TRDB |
Tandem repeats in genomic DNA |
http://tandem.bu.edu/cgi-bin/trdb/trdb.exe | |
| 1143 |
UgMicroSatdb |
UniGene MicroSatellite database: short tandem repeats from various eukaryotic genomes |
http://ipu.ac.in/usbt/UgMicroSatdb.htm | |
| 320 |
UniVec |
Vector sequences, adapters, linkers and primers used in DNA cloning, used to check for vector contamination |
http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html | |
| 252 |
UTRdb/UTRsite |
5'- and 3'-UTRs of eukaryotic mRNAs |
http://bighost.area.ba.cnr.it/BIG/UTRHome/ | |
| 1146 |
UTRome |
3'UTRs and their functional elements in C. elegans |
http://www.utrome.org | |
| 302 |
Vectordb |
Characterization and classification of nucleic acid vectors |
http://seq.yeastgenome.org/vectordb/ | |
| 968 |
VISTA Enhancer Browser |
Enhancer elements in the human genome |
http://enhancer.lbl.gov/ | |
| 1.3. Gene structure, introns and exons, splice sites |
| 414 |
ASAP II |
Comparative analysis of alternative splicing in animal species |
http://bioinfo.mbi.ucla.edu/ASAP2/ | |
| 10 |
ASDB |
Alternative Splicing Database: protein products and expression patterns of alternatively-spliced genes |
http://hazelton.lbl.gov/~teplitski/alt/ | |
| 639 |
ASHESdb |
Alternatively Spliced Human genes by Exon Skipping |
http://sege.ntu.edu.sg/wester/ashes/ | |
| 28 |
ASTD |
Alternative Splicing and Transcript Diversity database |
http://www.ebi.ac.uk/astd/ | |
| 920 |
ATD |
Alternate transcript diversity database |
Superseded by ASTD, no. 28 |
| 803 |
ChimerDB |
Chimeric (fusion) sequences in human, rat and mouse |
http://genome.ewha.ac.kr/ChimerDB/ | |
| 450 |
EASED |
Extended Alternatively Spliced EST Database |
http://eased.bioinf.mdc-berlin.de/ | |
| 667 |
ECgene |
Genome annotation for alternative splicing |
http://genome.ewha.ac.kr/ECgene/ | |
| 631 |
EDAS |
EST-derived alternative splicing database |
http://www.ig-msk.ru:8005/EDAS/ | |
| 32 |
EID |
Exon-intron database |
http://www.meduohio.edu/bioinfo/eid/ | |
| 34 |
ExInt |
Exon–intron structure of eukaryotic genes |
http://sege.ntu.edu.sg/wester/exint/ | |
| 913 |
ExtraTRAIN |
Extragenic regions and transcriptional regulators in bacteria and archaea |
http://www.era7.com/ExtraTrain/ | |
| 782 |
FUGOID |
Functional genomics of organelle introns database |
http://web.austin.utexas.edu/fugoid/introndata/main.htm | |
| 970 |
H-DBAS |
Human database of alternative splicing |
http://jbirc.jbic.or.jp/h-dbas/ | |
| 821 |
Hollywood |
Exon annotation database |
http://hollywood.mit.edu | |
| 36 |
HS3D |
Homo Sapiens Splice Sites Dataset |
http://www.sci.unisannio.it/docenti/rampone/ | |
| 238 |
Intronerator |
Alternative splicing in C. elegans and C. briggsae |
http://hgwdev-hiram.cse.ucsc.edu/IntronWS120/ | |
| 1122 |
ProSAS |
Protein Structure and Alternative Splicing: effects of alternative splicing events on protein structure |
http://services.bio.ifi.lmu.de/ProSAS | |
| 46 |
SpliceDB |
Canonical and non-canonical mammalian splice sites |
http://www.softberry.com/berry.phtml?topic=splicedb&group=data&subgroup=spldb | |
| 746 |
SpliceInfo |
Modes of alternative splicing in human genome |
http://spliceinfo.mbc.nctu.edu.tw/ | |
| 580 |
SpliceNest |
Visualizing Splicing of Genes from EST Data |
http://splicenest.molgen.mpg.de/ | |
| 927 |
TassDB |
TAndem Splice Site Database |
http://helios.informatik.uni-freiburg.de/TassDB/ | |
| 937 |
U12DB |
Database of orthologous U12-type spliceosomal introns |
http://genome.imim.es/cgi-bin/u12db/u12db.cgi | |
| 305 |
Xpro |
Eukaryotic protein-encoding DNA sequences, both intron-containing and intron-less genes |
http://origin.bic.nus.edu.sg/xpro/ | |
| 342 |
Yeast Intron Database |
Ares lab database of splicesomal introns in S. cerevisiae |
http://www.cse.ucsc.edu/research/compbio/yeast_introns.html | |
| 1.4. Transcriptional regulator sites and transcription factors |
| 795 |
ABS |
Annotated regulatory binding sites from orthologous promoters |
http://genome.imim.es/datasets/abs2005/ | |
| 231 |
ACTIVITY |
Functional DNA/RNA site activity |
http://wwwmgs.bionet.nsc.ru/mgs/systems/activity/ | |
| 308 |
ASPD |
Artificial selected proteins/peptides database |
http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/ | |
| 805 |
CisRed |
Human regulatory DNA sequence motifs |
http://www.cisred.org/ | |
| 1058 |
CMGSDB |
Computational models for gene silencing in C. elegans |
https://bioinformatics.cs.vt.edu/cmgs/CMGSDB/ | |
| 1062 |
COXPRESdb |
Coexpressed genes and networks in human and mouse |
http://coxpresdb.hgc.jp/ | |
| 1063 |
CTCF Binding Site DB |
Experimentally identified and predicted CTCF binding sties |
http://insulatordb.utmem.edu/ | |
| 807 |
DBD |
Transcription factor prediction database |
http://www.transcriptionfactor.org/ | |
| 31 |
DBTBS |
Bacillus subtilis promoters and transcription factors |
http://dbtbs.hgc.jp/ | |
| 591 |
DBTSS |
Database of transcriptional start sites |
http://dbtss.hgc.jp/ | |
| 663 |
DoOP |
Databases of Orthologous Promoters: chordates and plants |
http://doop.abc.hu/ | |
| 106 |
DPInteract |
Binding sites for E. coli DNA-binding proteins |
http://arep.med.harvard.edu/dpinteract/ | |
| 33 |
EPD |
Eukaryotic promoter database |
http://www.epd.isb-sib.ch/ | |
| 329 |
GeneNet |
Database on gene network components |
http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet/ | |
| 1036 |
GenomeTraFaC |
Conserved regulatory elements of human and mouse genes |
http://genometrafac.cchmc.org | |
| 823 |
HTPSELEX |
Transcription factor binding site sequences obtained using high-throughput SELEX method |
http://www.isrec.isb-sib.ch/htpselex/ | |
| 516 |
JASPAR |
PSSMs for transcription factor DNA-binding sites |
http://jaspar.cgb.ki.se | |
| 700 |
MAPPER |
Putative transcription factor binding sites in various genomes |
http://bio.chip.org/mapper | |
| 842 |
MPromDB |
Mammalian promoter database |
http://bioinformatics.med.ohio-state.edu/MPromDb | |
| 846 |
ODB |
Operon database |
http://odb.kuicr.kyoto-u.ac.jp/ | |
| 185 |
ooTFD |
Object-oriented transcription factors database |
http://www.ifti.org/ootfd | |
| 1107 |
ORegAnno |
Open REGulatory ANNOtation database |
http://www.oreganno.org/ | |
| 711 |
Osteo-Promoter DB |
Genes in osteogenic proliferation and differentiation |
http://www.opd.tau.ac.il | |
| 40 |
PLACE |
Plant cis-acting regulatory DNA elements |
http://www.dna.affrc.go.jp/PLACE/ | |
| 41 |
PlantCARE |
Plant promoters and cis-acting regulatory elements |
http://bioinformatics.psb.ugent.be/webtools/plantcare/html/ | |
| 563 |
PlantProm |
Plant promoter sequences for RNA polymerase II |
http://mendel.cs.rhul.ac.uk/mendel.php?topic=plantprom | |
| 1117 |
PlantTFDB |
Plant Transcription Factor Database |
http://planttfdb.cbi.pku.edu.cn | |
| 1005 |
PReMod |
Predicted transcriptional regulatory modules in the human genome |
http://genomequebec.mcgill.ca/PReMod | |
| 566 |
PRODORIC |
Prokaryotic database of gene regulation networks |
http://prodoric.tu-bs.de/ | |
| 42 |
PromEC |
E. coli promoters with experimentally-identified transcriptional start sites |
http://margalit.huji.ac.il/promec/ | |
| 1123 |
ProTISA |
Translation Initiation Site Annotation in prokaryotic genomes |
http://mech.ctb.pku.edu.cn/protisa/ | |
| 116 |
RegulonDB |
Transcriptional regulation and operon organization in E.coli |
http://regulondb.ccg.unam.mx/ | |
| 45 |
rSNP Guide |
SNPs in regulatory gene regions |
http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/ | |
| 577 |
SCPD |
Saccharomyces cerevisiae promoter database |
http://rulai.cshl.edu/SCPD/ | |
| 246 |
SELEXdb |
Selected DNA/RNA functional site sequences |
http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/ | |
| 1015 |
SwissRegulon database |
Genome-wide annotations of regulatory sites in the intergenic regions |
http://www.swissregulon.unibas.ch | |
| 227 |
TESS |
Transcription element search system |
http://www.cbil.upenn.edu/tess | |
| 904 |
TiProD |
Tissue-specific promoter database |
http://tiprod.cbi.pku.edu.cn:8080/index.html | |
| 756 |
Tractor_DB |
Transcription factors in gamma-proteobacteria database |
http://www.tractor.lncc.br | |
| 345 |
TRANSCompel® |
Transcriptional regulation, composite regulatory elements |
http://www.gene-regulation.com/pub/ databases.html#transcompel | |
| 340 |
TRANSFAC® |
Transcription factors, gene regulation, positional weight matrices |
http://www.gene-regulation.com | |
| 1141 |
TransfactomeDB |
Nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors |
http://bussemakerlab.org/YeastTransfactomeDB/ | |
| 341 |
TRANSPATH |
Signal transduction pathways, vizualization and expression data analysis |
http://www.biobase.de/pages/products/databases.html | |
| 48 |
Transterm |
Codon usage, start and stop signals |
http://guinevere.otago.ac.nz/transterm.html | |
| 757 |
TRED |
Transcriptional regulatory element database |
http://rulai.cshl.edu/tred | |
| 49 |
TRRD |
Transcription regulatory regions of eukaryotic genes |
http://www.bionet.nsc.ru/trrd/ | |
| 314 |
TrSDB |
Transcription factor database |
http://bioinf.uab.es/cgi-bin/trsdb/trsdb.pl | |
| 792 |
YEASTRACT |
Yeast transcriptional regulation |
http://www.yeastract.com | |
| 2. RNA Sequence, Structure and Functions |
| 229 |
16S and 23S rRNA Mutation Database |
16S and 23S ribosomal RNA mutations |
http://ribosome.fandm.edu | |
| 1041 |
3D rRNA modification maps |
Locations of modified rRNA nucleotides within the 3D structure of the ribosome |
http://people.biochem.umass.edu/fournierlab/3dmodmap/ | |
| 230 |
5S rRNA Database |
5S rRNA sequences |
http://biobases.ibch.poznan.pl/5SData/ | |
| 411 |
Aptamer Database |
Small RNA/DNA molecules binding nucleic acids, proteins |
http://aptamer.icmb.utexas.edu | |
| 232 |
ARED |
AU-rich element-containing mRNAs |
http://brp.kfshrc.edu.sa/ARED | |
| 797 |
Argonaute |
Gene regulation by mammalian microRNAs |
http://argonaute.uni-hd.de | |
| 984 |
dbRES |
Database of known RNA editing sites |
http://bioinfo.au.tsinghua.edu.cn/dbRES/ | |
| 463 |
European rRNA DB |
All complete or nearly complete rRNA sequences |
http://www.psb.ugent.be/rRNA/ | |
| 1027 |
fRNAdb |
Functional RNA Database: noncoding transcripts that affect gene expression |
http://www.ncrna.org/ | |
| 878 |
Greengenes |
Multiple sequence alignment of prokaryotic 16S rDNA |
http://greengenes.llnl.gov/16S/ | |
| 820 |
GRSDB |
G-rich sequences database |
http://bioinformatics.ramapo.edu/GRSDB2/ | |
| 490 |
G-tRNA-db |
Genomic tRNA Database |
http://lowelab.ucsc.edu/GtRNAdb/ | |
| 236 |
Guide RNA Database |
No longer maintained |
| 76 |
HIV Sequence DB |
HIV RNA sequences |
http://hiv-web.lanl.gov/ | |
| 689 |
HuSiDa |
Human siRNA database |
http://itb.biologie.hu-berlin.de/~nebulus/sirna/index.htm | |
| 237 |
HyPaLib |
Hybrid pattern library: structural elements in classes of RNA |
Not actively maintained |
| 379 |
IRESdb - |
the Internal Ribosome Entry Site database |
http://ifr31w3.toulouse.inserm.fr/IRESdatabase/ | |
| 831 |
IRESite |
Experimentally studied internal ribosome entry sites |
http://www.iresite.org | |
| 838 |
MeRNA |
Metal ion binding sites in RNA |
http://merna.lbl.gov | |
| 1097 |
microRNA.org |
microRNA target predictions and expression profiles |
http://www.microrna.org | |
| 529 |
miRBase |
MicroRNA sequences, names, and predicted targets in animals |
http://microrna.sanger.ac.uk/sequences/ | |
| 1098 |
miRGator |
microRNA target prediction, functional analysis, and gene expression data |
http://genome.ewha.ac.kr/miRGator/miRGator.html | |
| 994 |
miRGen |
Animal microRNAs located in introns, exons, UTRs, pseudogenes and CpG islands |
http://www.diana.pcbi.upenn.edu/miRGen | |
| 895 |
miRNAMap |
microRNA precursors and their mapping to targets in vertebrate genomes |
http://mirnamap.mbc.nctu.edu.tw | |
| 378 |
Mobile group II introns |
Database for mobile group II introns |
http://www.fp.ucalgary.ca/group2introns/ | |
| 840 |
MODOMICS |
Database of RNA modification pathways |
http://genesilico.pl/modomics/ | |
| 997 |
NATsDB |
Natural Antisense Transcripts database |
http://nats.cbi.pku.edu.cn | |
| 380 |
NCIR |
Non-Canonical Interactions in RNA |
http://prion.bchs.uh.edu/bp_type/ | |
| 381 |
ncRNAs database |
Non-coding RNAs with regulatory functions |
http://biobases.ibch.poznan.pl/ncRNA/ | |
| 705 |
NONCODE |
Database of noncoding RNAs |
http://bioinfo.ibp.ac.cn/NONCODE/index.htm | |
| 845 |
NPInter |
Noncoding RNA-protein interactions |
http://bioinfo.ibp.ac.cn/NPInter/index.php | |
| 1114 |
piRNABank |
Sequences and properties of Piwi-interacting RNAs (piRNAs) in human, mouse and rat |
http://pirnabank.ibab.ac.in/ | |
| 564 |
Plant snoRNA DB |
snoRNA genes in plant species |
http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home | |
| 240 |
PLANTncRNAs |
No longer maintained |
| 241 |
PLMItRNA |
Mitochondrial tRNA genes in photosynthetic eukaryotes |
http://bighost.area.ba.cnr.it/PLMItRNA/ | |
| 723 |
PolyA_DB |
Database of mammalian mRNA polyadenylation |
http://polya.umdnj.edu/ | |
| 242 |
PseudoBase |
Database of RNA pseudoknots |
http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html | |
| 1009 |
REDIdb |
An RNA editing database |
http://biologia.unical.it/py_script/search.html | |
| 382 |
Rfam |
Non-coding RNA families |
http://www.sanger.ac.uk/Software/Rfam/ | |
| 243 |
RDP-II |
Ribosomal Database Project |
http://rdp.cme.msu.edu | |
| 244 |
RISSC |
Ribosomal Internal Spacer Sequence Collection |
http://egg.umh.es/rissc | |
| 245 |
RNA Modification DB |
Naturally modified nucleosides in RNA |
http://medlib.med.utah.edu/RNAmods/ | |
| 900 |
RNA SSTRAND |
RNA secondary structure data and structural motifs |
http://www.rnasoft.ca/sstrand | |
| 630 |
RNAdb |
Mammalian noncoding RNA database |
http://ncrna.bioinformatics.com.au | |
| 862 |
RNAi codex |
Clones from mouse, human and rat shRNA libraries |
http://codex.cshl.org | |
| 1162 |
siRecords |
Experimentally tested mammalian siRNAs |
http://sirecords.umn.edu/siRecords/ | |
| 629 |
siRNAdb |
Functional human siRNA sequences |
http://sirna.cgb.ki.se | |
| 247 |
Small RNA Database |
No longer maintained |
| 869 |
snoRNA-LBME-db |
Human snoRNAs and Cajal body-specific RNAs (scaRNAs) |
http://www-snorna.biotoul.fr/ | |
| 962 |
Sno/scaRNAbase |
Small nucleolar RNAs and cajal body-specific RNAs |
http://gene.fudan.sh.cn/snoRNAbase.nsf | |
| 248 |
SRPDB |
Signal recognition particle database |
http://rnp.uthct.edu/rnp/SRPDB/SRPDB.html | |
| 383 |
Subviral RNA DB |
Database of viroids and viroid-like RNAs |
http://subviral.med.uottawa.ca/ | |
| 754 |
The Small Subunit rRNA Modification DB |
Modified nucleosides in small subunit rRNA |
http://library.med.utah.edu/SSUmods/ | |
| 250 |
tmRDB |
tmRNA database |
http://rnp.uthct.edu/rnp/tmRDB/tmRDB.html | |
| 249 |
tmRNA Website |
tmRNA sequences and alignments |
http://www.indiana.edu/~tmrna | |
| 251 |
tRNA Sequences |
Has not been updated |
| 1148 |
Vir-Mir db |
Prediction of viral microRNA candidate hairpins |
http://alk.ibms.sinica.edu.tw | |
| 254 |
Yeast snoRNA Database |
Yeast small nucleolar RNAs |
http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html | |
| 3. Protein Sequence Databases |
| 3.1. General sequence databases |
| 163 |
EXProt |
Sequences of proteins with experimentally verified function |
http://www.cmbi.kun.nl/EXProt/ | |
| 88 |
MIPS resources |
Munich Information Center for Protein Sequences databases |
http://mips.gsf.de/ | |
| 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/ | |
| 194 |
PIR |
Protein Information Resource |
http://pir.georgetown.edu | |
| 565 |
PRF |
Protein research foundation database of peptides |
http://www.prf.or.jp/en/index.shtml | |
| 790 |
TCDB |
Transporter protein classification database |
http://www.tcdb.org/ | |
| 775 |
UniParc |
UniProt archive, a repository of all protein sequences |
http://www.uniprot.org/database/archive.shtml | |
| 318 |
UniProt |
Universal Protein knowledgebase, combined information from Swiss-Prot, TrEMBL, and PIR |
http://www.uniprot.org | |
| 197 |
UniProtKB\Swiss-Prot |
Formerly SwissProt, part of the UniProt knowledgebase |
http://www.expasy.org/sprot | |
| 198 |
UniProtKB\TrEMBL |
Now UniProt/TrEMBL, part of the UniProt knowledgebase |
http://www.uniprot.org/database/knowledgebase.shtml | |
| 776 |
UniRef |
Clustered sets of related sequences from UniProt |
http://www.uniprot.org/database/nref.shtml | |
| 1165 |
UniSave |
UniProtKB Sequence/Annotation Version Archive |
http://www.ebi.ac.uk/uniprot/unisave/ | |
| 3.2. Protein properties |
| 221 |
AAindex |
Physicochemical properties of amino acids |
http://www.genome.ad.jp/aaindex/ | |
| 979 |
BindingDB |
Binding affinities of protein-ligand and other complexes |
http://www.bindingdb.org/bind/index.jsp | |
| 806 |
CyBase |
Proteins with cyclic backbones |
http://research1t.imb.uq.edu.au/cybase | |
| 885 |
dbPTM |
Information on post-translational modification of proteins |
http://dbptm.mbc.nctu.edu.tw/ | |
| 914 |
iProLINK |
Annotated literature sources for protein features and names |
http://pir.georgetown.edu/iprolink | |
| 1093 |
MALISAM |
Manual alignments for structurally analogous motifs in proteins |
http://prodata.swmed.edu/malisam | |
| 1094 |
MegaMotifbase |
Structural motifs in protein families and superfamilies |
http://caps.ncbs.res.in/MegaMotifbase/index.html | |
| 954 |
PIDD |
Protein inter-atomic distances database |
http://pidd.math.iastate.edu | |
| 854 |
PINT |
Protein-protein interactions thermodynamic database |
http://pintdb.dyndns.org/index.html | |
| 856 |
PPD |
Experimentally-determined protein pKa values |
http://www.jenner.ac.uk/ppd/ | |
| 1120 |
PPT-DB |
Protein Property Prediction and Testing Database |
http://redpoll.pharmacy.ualberta.ca/PPT_DB/public_html/PPT_main.html | |
| 280 |
ProTherm |
Thermodynamic data for wild-type and mutant proteins |
http://gibk26.bse.kyutech.ac.jp/jouhou/protherm/protherm.html | |
| 1176 |
PRTAD |
Protein residue torsion angle database |
http://www.math.iastate.edu/prtad | |
| 783 |
REFOLD |
Experimental data on protein refolding and purification |
http://refold.med.monash.edu.au | |
| 3.3. Protein localization and targeting |
| 444 |
DBSubLoc - |
Database of protein Subcellular Localization |
http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html | |
| 930 |
eSLDB |
eukaryotic proteins Subcellular Localization Database |
http://gpcr.biocomp.unibo.it/esldb | |
| 1021 |
InterFil |
Human Intermediate Filament database |
http://www.interfil.org | |
| 836 |
LOCATE |
Subcellular localization of mouse proteins |
http://locate.imb.uq.edu.au/ | |
| 1022 |
MiCroKit |
Midbody, Centrosome and Kinetochore proteins |
http://bioinformatics.lcd-ustc.org/microkit/ | |
| 226 |
MitoDrome |
Nuclear-encoded mitochondrial proteins of Drosophila |
http://www2.ba.itb.cnr.it/MitoDrome/ | |
| 85 |
MitoRes |
Nuclear genes coding for mitochondrial proteins |
http://www2.ba.itb.cnr.it/MitoNuc/ | |
| 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/ | |
| 369 |
NPD |
Nuclear Protein Database |
http://npd.hgu.mrc.ac.uk | |
| 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/nurebase.html | |
| 789 |
NURSA |
Nuclear receptor signaling atlas |
http://www.nursa.org | |
| 734 |
PSORTdb |
Protein subcellular localization in bacteria |
http://db.psort.org/ | |
| 745 |
Secreted Protein DB |
Secreted proteins from human, mouse and rat |
http://spd.cbi.pku.edu.cn | |
| 1014 |
SUBA |
Subcellular localisation of Arabidopsis proteins |
http://www.suba.bcs.uwa.edu.au/ | |
| 587 |
THGS |
Transmembrane Helices in Genome Sequences |
http://pranag.physics.iisc.ernet.in/thgs/ | |
| 1140 |
TopDB |
Topology Data Bank of transmembrane proteins |
http://topdb.enzim.hu | |
| 589 |
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 |
| 374 |
ASC |
Active Sequence Collection |
http://bioinformatica.isa.cnr.it/ASC/ | |
| 203 |
Blocks |
Alignments of conserved regions in protein families |
http://blocks.fhcrc.org | |
| 438 |
COMe |
Co-Ordination of Metals etc. |
http://www.ebi.ac.uk/come/ | |
| 771 |
CoPS |
Comprehensive peptide signature database |
http://cops.igib.res.in/copsv2/index.html | |
| 440 |
CSA |
Catalytic Site Atlas |
http://www.ebi.ac.uk/thornton-srv/databases/CSA/ | |
| 666 |
eBLOCKS |
Highly conserved protein sequence blocks |
http://fold.stanford.edu/eblocks/acsearch.html | |
| 452 |
eF-site |
Electrostatic surface of Functional site |
http://ef-site.protein.osaka-u.ac.jp/eF-site | |
| 206 |
eMOTIF |
Protein sequence motif determination and searches |
http://motif.stanford.edu/emotif | |
| 986 |
FireDB |
Functionally important residues in protein structures |
http://firedb.bioinfo.cnio.es/ | |
| 207 |
InterPro |
Integrated resource of protein families, domains and functional sites |
http://www.ebi.ac.uk/interpro | |
| 179 |
Metalloprotein Site DB |
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/srs6bin/cgi-bin/wgetz?-page+LibInfo+-newId+-lib+PDBSite | |
| 187 |
Phospho.ELM |
S/T/Y protein phosphorylation sites (former PhosphoBase) |
http://phospho.elm.eu.org/ | |
| 1003 |
Phospho3D |
3D structures of protein phosphorylation sites |
http://cbm.bio.uniroma2.it/p3d/ | |
| 212 |
PRINTS |
Hierarchical gene family fingerprints |
http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/ | |
| 193 |
PROMISE |
Prosthetic centers and metal ions in protein active sites |
http://metallo.scripps.edu/PROMISE/ | |
| 899 |
ProRule |
Functional and structural information on PROSITE profiles |
http://www.expasy.org/prosite/prorule.html | |
| 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 | |
| 868 |
SitesBase |
Known ligand binding sites in the PDB |
http://www.modelling.leeds.ac.uk/sb/ | |
| 3.5. Protein domain databases; protein classification |
| 622 |
ADDA |
Database of protein domain classification |
http://ekhidna.biocenter.helsinki.fi/sqgraph/pairsdb | |
| 288 |
BAliBASE |
Benchmark database for comparison of multiple sequence alignments |
http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html | |
| 978 |
Benchmark |
Protein classification benchmark collection: training/test sets for machine learning |
http://net.icgeb.org/benchmark/ | |
| 786 |
BIOZON |
Database of gene and protein familiy classification |
http://biozon.org | |
| 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 UniProt Knowledgebase and IPI proteins |
http://www.ebi.ac.uk/clustr/ | |
| 7 |
COG |
Clusters of orthologous groups of proteins |
http://www.ncbi.nlm.nih.gov/COG | |
| 448 |
DomIns |
Database of Domain Insertions |
http://www.domins.org/ | |
| 1068 |
eggNOG |
Evolutionary genealogy of genes: Non-supervised Orthologous Groups |
http://eggnog.embl.de | |
| 1069 |
EPGD |
Eukaryotic Paralog Group Database |
http://epgd.biosino.org:8080/EPGD/ | |
| 963 |
EVEREST |
Automatically generated protein domain families |
http://www.everest.cs.huji.ac.il | |
| 671 |
FunShift |
Functional divergence between the subfamilies of a protein domain family |
http://FunShift.cgb.ki.se | |
| 470 |
FusionDB |
Database of bacterial and archaeal gene fusion events |
http://www.igs.cnrs-mrs.fr/FusionDB/ | |
| 200 |
Hits |
Database of protein domains and motifs |
http://hits.isb-sib.ch | |
| 266 |
HSSP |
Homology-derived structures of proteins |
http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-page+LibInfo+-lib+HSSP | |
| 510 |
InterDom |
Putative protein domain interactions |
http://interdom.i2r.a-star.edu.sg/ | |
| 208 |
iProClass |
Integrated protein classification database |
http://pir.georgetown.edu/iproclass/ | |
| 844 |
MulPSSM |
Multiple PSSMs of structural and sequence families |
http://hodgkin.mbu.iisc.ernet.in/~mulpssm | |
| 1109 |
PairsDB |
Pairwise alignments of all sequences in UniProt |
http://pairsdb.csc.fi | |
| 274 |
PALI |
Phylogeny and alignment of homologous protein structures |
http://pauling.mbu.iisc.ernet.in/~pali | |
| 552 |
PANTHER |
Protein sequence evolution mapped to functions and pathways |
http://www.pantherdb.org | |
| 210 |
Pfam |
Protein families: Multiple sequence alignments and profile hidden Markov models of protein domains |
http://pfam.sanger.ac.uk/ | |
| 981 |
PhyloFacts |
Phylogenomic analysis of protein families |
http://phylogenomics.berkeley.edu/phylofacts/ | |
| 561 |
PIRSF |
Family/superfamily classification of whole proteins |
http://pir.georgetown.edu/pirsf/ | |
| 214 |
ProDom |
Protein domain families |
http://prodom.prabi.fr/ | |
| 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/ | |
| 217 |
SBASE |
Protein domain sequences and tools |
http://www.icgeb.org/sbase | |
| 867 |
SIMAP |
Similarity matrix of proteins: precomputed similarity data |
http://mips.gsf.de/simap/ | |
| 1010 |
SISYPHUS |
Structural alignments for proteins with non-trivial relationships |
http://sisyphus.mrc-cpe.cam.ac.uk | |
| 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 | |
| 199 |
TIGRFAMs |
TIGR protein families adapted for functional annotation |
http://www.tigr.org/TIGRFAMs | |
| 3.6. Databases of individual protein families |
| 157 |
ABCdb |
Archaeal and bacterial ABC transporter database |
http://www-abcdb.biotoul.fr | |
| 156 |
Aminoacyl-tRNA synthetases database |
Aminoacyl-tRNA synthetase database |
http://rose.man.poznan.pl/aars/index.html | |
| 1045 |
Animal Toxin DB |
Database of animal toxins |
http://protchem.hunnu.edu.cn/toxin | |
| 412 |
ARAMEMNON |
Arabidopsis thaliana membrane proteins and transporters |
http://aramemnon.botanik.uni-koeln.de | |
| 1166 |
BACTIBASE |
Database of bacteriocin natural antimicrobial peptides |
http://www.pfba-lab.org/bactibase | |
| 158 |
BacTregulators |
Transcriptional regulators of AraC and TetR families |
No longer maintained |
| 976 |
BANMOKI |
Database of bacterial nucleoside monophosphate kinases |
http://www.ces.clemson.edu/compbio/databases/kinases | |
| 1057 |
ChromDB |
Chromatin-associated proteins in a broad range of organisms |
http://www.chromdb.org | |
| 923 |
cpnDB |
Chaperonin database |
http://cpndb.cbr.nrc.ca/ | |
| 1154 |
CREMOFAC |
Database of chromatin remodeling factors |
http://www.jncasr.ac.in/cremofac/ | |
| 364 |
CSDBase |
Cold Shock Domain database |
http://www.chemie.uni-marburg.de/~csdbase/ | |
| 1168 |
CyMoBase |
Cytoskeletal and motor proteins database |
http://www.motorprotein.de/cymobase | |
| 1065 |
DB-PABP |
Experimentally characterized polyanion-binding proteins |
http://ppa.bcf.ku.edu/DB_PABP/ | |
| 658 |
DCCP |
Database of Copper-Chelating Proteins |
http://sdbi.sdut.edu.cn/DCCP/en/index.php | |
| 945 |
Defensins Knowledgebase |
Antimicrobial peptides of the defensin family |
http://defensins.bii.a-star.edu.sg/ | |
| 160 |
DExH/D Family DB |
DEAD-box, DEAH-box and DExH-box proteins |
http://www.helicase.net/dexhd/dbhome.htm | |
| 892 |
DSD |
Database of dehydrogenase stereospecificities |
http://www.jenner.ac.uk/DSD | |
| 161 |
Endogenous GPCR List |
G protein-coupled receptors; expression in cell lines |
http://www.tumor-gene.org/GPCR/gpcr.html | |
| 814 |
EROP-Moscow |
Database of Endogenous Regulatory OligoPeptides |
http://erop.inbi.ras.ru | |
| 162 |
ESTHER |
Esterases and other alpha/beta hydrolase enzymes |
http://bioweb.ensam.inra.fr/ESTHER/general?what=index | |
| 164 |
FUNPEP |
Low-complexity peptides capable of forming amyloid plaque |
http://www.cmbi.kun.nl/swift/FUNPEP/gergo/ | |
| 166 |
GPCRDB |
G protein-coupled receptors database |
http://www.gpcr.org/7tm/ | |
| 679 |
gpDB |
G-protein database: G-proteins and their interaction with GPCRs |
http://bioinformatics.biol.uoa.gr/gpDB | |
| 1085 |
Heme Protein DB |
Heme protein structure, heme type, axial ligands, and heme protein reduction potential (Em) values |
http://heme.chem.columbia.edu/heme.php | |
| 167 |
Histone Database |
Histone fold sequences and structures |
http://research.nhgri.nih.gov/histones/ | |
| 365 |
HIV RT and Protease Sequence Database |
HIV reverse transcriptase and protease sequences |
http://hivdb.stanford.edu | |
| 169 |
Homeobox Page |
Homeobox proteins, classification, and evolution |
http://www.biosci.ki.se/groups/tbu/homeo.html | |
| 170 |
Homeodomain Resource |
Homeodomain sequences, structures, and related genetic and genomic information |
http://research.nhgri.nih.gov/homeodomain/ | |
| 174 |
InBase |
Inteins (protein splicing elements) database: properties, sequences, bibliography |
http://www.neb.com/neb/inteins.html | |
| 518 |
KinG |
Kinases in Genomes: Ser/Thr/Tyr kinases encoded in the completely sequenced genomes |
http://hodgkin.mbu.iisc.ernet.in/~king | |
| 519 |
Knottin database |
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 DB |
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/ | |
| 1105 |
NORINE |
Database of nonribosomal peptides |
http://bioinfo.lifl.fr/norine/ | |
| 546 |
NucleaRDB |
Nuclear receptor superfamily |
http://www.receptors.org/NR/ | |
| 184 |
Olfactory Receptor DB |
Sequences for olfactory receptor-like molecules |
http://senselab.med.yale.edu/senselab/ordb/ | |
| 186 |
Peptaibol |
Peptaibol (antibiotic peptide) sequences |
http://www.cryst.bbk.ac.uk/peptaibol/ | |
| 560 |
PhytoProt |
Clusters of (predicted) plant proteins |
http://urgi.versailles.inra.fr/phytoprot/ | |
| 189 |
PLANT-PIs |
Plant protease inhibitors |
http://bighost.area.ba.cnr.it/PLANT-Pis | |
| 371 |
PlantsP/PlantsT |
Plant proteins involved in phosphorylation and transport |
http://plantsp.sdsc.edu | |
| 759 |
PLPMDB |
Pyridoxal-5'-phosphate dependent enzymes mutations |
http://www.studiofmp.com/plpmdb/ | |
| 609 |
ProLysED |
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/ | |
| 188 |
Protein kinase resource |
Protein kinase resource: sequences, enzymology, genetics and molecular and structural properties |
http://www.kinasenet.org/pkr/ | |
| 224 |
REBASE |
Restriction enzymes and associated methylases |
http://rebase.neb.com/rebase/rebase.html | |
| 195 |
RNAse P Database |
Ribonuclease P sequences, alignments and structures |
http://www.mbio.ncsu.edu/RNaseP/home.html | |
| 901 |
RNRdb |
Ribonucleotide reductase database |
http://rnrdb.molbio.su.se/ | |
| 573 |
RPG |
Ribosomal Protein Gene database |
http://ribosome.miyazaki-med.ac.jp/ | |
| 575 |
RTKdb |
Receptor Tyrosine Kinase database |
http://pbil.univ-lyon1.fr/RTKdb/ | |
| 372 |
SDAP |
Structural database of allergenic proteins and food allergens |
http://fermi.utmb.edu/SDAP | |
| 1131 |
SelenoDB |
Database of selenoprotein genes, proteins and SECIS elements |
http://www.selenodb.org/ | |
| 196 |
SENTRA |
Sensory signal transduction proteins |
http://compbio.mcs.anl.gov/sentra/ | |
| 373 |
SEVENS |
7-transmembrane helix receptors (G-protein-coupled) |
http://sevens.cbrc.jp/1.20/ | |
| 1137 |
Telomerase database |
Sequences and structures of the RNA and protein subunits of telomerase, mutations of telomerase components |
http://telomerase.asu.edu | |
| 311 |
TransportDB |
Predicted membrane transporters in complete genomes, classified according to the TC classification system |
http://www.membranetransport.org | |
| 399 |
VKCDB |
Voltage-gated K+ Channel Database |
http://vkcdb.biology.ualberta.ca/ | |
| 202 |
Wnt Database |
Wnt proteins and phenotypes |
http://www.stanford.edu/~rnusse/wntwindow.html | |
| 4. Structure Databases |
| 4.1. Small molecules |
| 402 |
AANT |
Amino Acid - Nucleotide interaction database |
http://aant.icmb.utexas.edu/ | |
| 646 |
ChEBI |
Chemical entities of biological interest |
http://www.ebi.ac.uk/chebi/ | |
| 1024 |
ChemBank |
Structures and biological activities of small organic molecules |
http://chembank.broad.harvard.edu/ | |
| 1023 |
ChemDB |
3D structures and properties of small molecules |
http://cdb.ics.uci.edu | |
| 261 |
CSD |
Cambridge Structural Database |
http://www.ccdc.cam.ac.uk/prods/csd/csd.html | |
| 360 |
Het-PDB Navi |
Hetero-atoms in protein structures |
http://daisy.bio.nagoya-u.ac.jp/golab/hetpdbnavi.html | |
| 265 |
HIC-Up |
Hetero-compound Information Centre - Uppsala |
http://xray.bmc.uu.se/hicup/ | |
| 111 |
Klotho |
Collection and categorization of biological compounds |
http://www.biocheminfo.org/klotho/ | |
| 113 |
LIGAND |
Chemical compounds and reactions in biological pathways |
http://www.genome.ad.jp/ligand/ | |
| 615 |
PDB-Ligand |
3D structures of small molecules bound to proteins and nucleic acids |
http://www.idrtech.com/PDB-Ligand/ | |
| 735 |
PubChem |
Structures and biological activities of small organic molecules |
http://pubchem.ncbi.nlm.nih.gov/ | |
| 1127 |
R.E.DD.B. |
RESP and ESP atomic charges and force field libraries for small molecules and molecular fragments |
http://q4md-forcefieldtools.org/REDDB | |
| 4.2. Carbohydrates |
| 977 |
BCSDB/Glycoscience |
Bacterial Carbohydrate Structure DataBase |
http://www.glyco.ac.ru/bcsdb/start.shtml | |
| 429 |
CarbBank |
CCSD - Complex Carbohydrate Structure Database |
http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm | |
| 652 |
CSS |
Carbohydrate Structure Suite: carbohydrate 3D structures |
http://www.dkfz.de/spec/css/ | |
| 486 |
Glycan |
Carbohydrate database, part of the KEGG system |
http://glycan.genome.ad.jp/ | |
| 1080 |
Glycoconjugate Data Bank |
Annotated structures of glycan molecules |
http://daisy2.nagahama-i-bio.ac.jp/structures/ | |
| 988 |
GlycoMaps DB |
Conformational maps of disaccharides |
http://www.glycosciences.de/modeling/glycomapsdb/ |
| 292 |
GlycoSuiteDB |
N- and O-linked glycan structures and biological sources |
http://www.glycosuite.com | |
| 535 |
Monosaccharide Browser |
Space filling Fischer projections of monosaccharides |
http://www.terravivida.com/vivida/monosaccharide/ | |
| 300 |
SWEET-DB |
Annotated carbohydrate structure and substance information |
http://www.dkfz-heidelberg.de/spec2/sweetdb/ | |
| 4.3. Nucleic acid structure |
| 1082 |
Greglist |
G-quadruplex motifs and potentially G-quadruplex regulated genes |
http://tubic.tju.edu.cn/greglist/ | |
| 1090 |
ITS2 |
Predicted structures of internal transcribed spacer 2 (ITS2) molecules |
http://its2.bioapps.biozentrum.uni-wuerzburg.de/ITS2_db.html | |
| 272 |
NDB |
Nucleic acid-containing structures |
http://ndbserver.rutgers.edu/ | |
| 273 |
NTDB |
Thermodynamic data for nucleic acids |
http://ntdb.chem.cuhk.edu.hk | |
| 1126 |
QuadBase |
G-quadruplex motifs in the promoters of human, chimpanzee, rat, mouse and bacterial genes |
http://quadbase.igib.res.in/ | |
| 1129 |
RNA FRABASE |
Database of 3D RNA fragments within known RNA structures |
http://rnafrabase.ibch.poznan.pl/ | |
| 387 |
RNABase |
RNA-containing structures from PDB and NDB |
http://www.rnabase.org | |
| 1130 |
RNAJunction |
RNA structural elements: helical junctions, internal loops, bulges and loop-loop interactions |
http://rnajunction.abcc.ncifcrf.gov | |
| 908 |
SARS-CoV RNA SSS |
Predicted secondary structures of SARS coronavirus RNA |
http://www.liuweibo.com/sarsdb/ | |
| 283 |
SCOR |
Structural classification of RNA: RNA motifs by structure, function and tertiary interactions |
http://scor.lbl.gov | |
| 4.4. Protein structure |
| 401 |
3D-Genomics |
Structural annotations for complete proteomes |
http://www.sbg.bio.ic.ac.uk/3dgenomics | |
| 633 |
3DID |
3D interacting domains |
http://gatealoy.pcb.ub.es/3did/ | |
| 413 |
ArchDB |
Automated classification of protein loop structures |
http://gurion.imim.es/archdb | |
| 255 |
ASTRAL |
Sequences of domains of known structure, selected subsets and sequence-structure correspondences |
http://astral.berkeley.edu/ | |
| 1047 |
AutoPSI |
Automated structural classification of protein sequences |
http://www.bio.ifi.lmu.de/AutoPSIDB | |
| 257 |
BioMagResBank |
NMR spectroscopic data from proteins, peptides, and nucleic acids |
http://www.bmrb.wisc.edu/ | |
| 384 |
CADB |
Conformational Angles DataBase of Proteins |
http://cluster.physics.iisc.ernet.in/cadb/ | |
| 258 |
CATH |
Protein domain structures database |
http://www.cathdb.info/ | |
| 259 |
CE |
Combinatorial Extension method to compute and review 3D protein structure alignments |
http://cl.sdsc.edu/ce.html | |
| 260 |
CKAAPs DB |
Conserved Key Amino Acid Positions Database |
No longer maintained |
| 882 |
CoC Central |
Universally conserved residues in protein folds |
http://kulibin.mit.edu/coc/ | |
| 1059 |
ColiSNP |
Mapping non-synonymous SNPs on protein structures |
http://yayoi.kansai.jaea.go.jp/colisnp | |
| 883 |
Columba |
Annotation of protein structures from the PDB |
http://www.columba-db.de | |
| 442 |
Dali database |
Fold classification based on structural alignment of proteins |
http://ekhidna.biocenter.helsinki.fi/dali/start | |
| 1169 |
DBAli |
Database of structure alignments |
http://salilab.org/DBAli/ | |
| 385 |
Decoys-R-Us |
Computer-generated protein conformations based on sequence data |
http://dd.compbio.washington.edu/ | |
| 447 |
DisProt |
Database of Protein Disorder |
http://divac.ist.temple.edu/disprot | |
| 809 |
DMAPS |
Database of multiple alignments for protein structures |
http://bioinformatics.albany.edu/~dmaps | |
| 264 |
DSDBASE |
Disulfide Database |
http://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.html | |
| 386 |
DSMM |
A Database of Simulated Molecular Motions |
http://projects.villa-bosch.de/dbase/dsmm/ | |
| 456 |
E-MSD |
EBI-Macromolecular Structure Database |
http://www.ebi.ac.uk/msd | |
| 818 |
FSN |
Flexible structural neighborhood, structural neighbors of proteins identified by FATCAT tool |
http://fatcat.ljcrf.edu/fatcat-cgi/cgi/struct_neibor/fatcatStructNeibor.pl | |
| 469 |
FSSP |
Superseded by the Dali database, no. 442 |
| 472 |
Gene3D |
Precalculated structural assignments for whole genomes |
http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/ | |
| 489 |
Genomic Threading DB |
Structural annotations of complete genomes |
http://bioinf.cs.ucl.ac.uk/GTD | |
| 322 |
GTOP |
Protein fold predictions from genome sequences |
http://spock.genes.nig.ac.jp/~genome/gtop.html | |
| 498 |
HOMSTRAD |
Homologous structure alignment database: curated structure-based alignments for protein families |
http://www-cryst.bioc.cam.ac.uk/homstrad | |
| 267 |
IMB Jena Image Library |
Visualization and analysis of 3D biopolymer structures |
http://www.imb-jena.de/IMAGE.html | |
| 502 |
IMGT/3Dstructure-DB |
3D structures of Immunoglobulins, T cell receptors, and MHC proteins |
http://imgt3d.igh.cnrs.fr/ | |
| 829 |
IMOTdb |
Spatially interacting motifs in proteins |
http://caps.ncbs.res.in/imotdb/ | |
| 269 |
LPFC |
Library of protein family core structures |
http://helix-web.stanford.edu/LPFC/ | |
| 270 |
MMDB |
All experimentally-determined 3D structures, linked to NCBI Entrez |
http://www.ncbi.nlm.nih.gov/Structure/ | |
| 331 |
ModBase |
Annotated comparative protein structure models |
http://salilab.org/modbase | |
| 262 |
MolMovDB |
Database of Macromolecular Movements |
http://bioinfo.mbb.yale.edu/MolMovDB/ | |
| 107 |
MPID |
MHC-Peptide Interaction Database |
http://surya.bic.nus.edu.sg/mpidt | |
| 275 |
PASS2 |
Structural motifs of protein superfamilies |
http://www.ncbs.res.in/~faculty/mini/campass/pass2.html | |
| 276 |
PDB |
Protein Data Bank: all known protein structures |
http://www.pdb.org/ | |
| 619 |
PDB_TM |
Transmembrane proteins with known 3D structure |
http://pdbtm.enzim.hu/ | |
| 277 |
PDB-REPRDB |
Representative protein chains, based on PDB entries |
http://mbs.cbrc.jp/pdbreprdb-cgi/reprdb_menu.pl | |
| 278 |
PDBsum |
Summaries and analyses of PDB structures |
http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/ | |
| 557 |
PepConfDB |
Database of peptide conformations |
http://www.peptidome.org/products/list.htm | |
| 719 |
PFD |
Protein Folding Database : Experimental data on protein folding |
http://www.foldeomics.org/pfd/public_html/index.php | |
| 855 |
PMDB |
3D protein models obtained from structure predictions |
http://www.caspur.it/PMDB/ | |
| 281 |
RESID |
Post-translational modifications of proteins |
http://www.ebi.ac.uk/RESID/ | |
| 740 |
S4 |
Structure-based Sequence Alignments of SCOP Superfamilies |
http://compbio.mds.qmw.ac.uk/~james/S4.shtml | |
| 282 |
SCOP |
Structural classification of proteins |
http://scop.mrc-lmb.cam.ac.uk/scop | |
| 863 |
SCOPPI |
Structural classification of protein-protein interfaces |
http://www.scoppi.org | |
| 284 |
SLoop |
Classification of protein loops |
http://www-cryst.bioc.cam.ac.uk/~sloop/ | |
| 530 |
SSToSS |
Sequence-Structural Templates of Single-member Superfamilies |
http://caps.ncbs.res.in/SSTOSS/index.htm | |
| 785 |
STING Report |
Amino acid properties in proteins of known structure |
http://sms.cbi.cnptia.embrapa.br/SMS/STINGm/SMSReport/ | |
| 583 |
Structure Superposition Database |
Pairwise superpositions of 115 TIM-barrel structures |
http://ssd.rbvi.ucsf.edu/ | |
| 285 |
SUPERFAMILY |
Assignments of proteins to structural superfamilies |
http://supfam.org/SUPERFAMILY/ | |
| 584 |
SURFACE |
Surface residues and functions annotated, compared and evaluated: a database of protein surface patches |
http://cbm.bio.uniroma2.it/surface | |
| 585 |
SWISS-MODEL Repository |
3D protein structure models generated by automated homology modeling using SWISS-MODEL |
http://swissmodel.expasy.org/repository | |
| 764 |
TargetDB |
Target data from worldwide structural genomics projects |
http://targetdb.pdb.org/ | |
| 938 |
TMBETA-GENOME |
Beta-barrel membrane proteins encoded in various genomes |
http://tmbeta-genome.cbrc.jp/annotation/ | |
| 941 |
TOPOFIT-DB |
Protein structural alignments based on the TOPOFIT method |
http://mozart.bio.neu.edu/topofit/ | |
| 310 |
TOPS |
Topology Of Protein Structures |
http://www.tops.leeds.ac.uk | |
| 5. Genomics Databases (non-human) |
| 5.1. Genome annotation terms, ontologies and nomenclature |
| 915 |
BioThesaurus |
A collection of gene/protein names and associated sequences |
http://pir.georgetown.edu/iprolink/biothesaurus | |
| 1075 |
FunSimMat |
Gene Ontology-based functional similarity values for proteins and protein families |
http://gotax.bioinf.mpi-inf.mpg.de/funsimmat/ | |
| 487 |
GO |
Gene ontology consortium database |
http://www.geneontology.org/ | |
| 389 |
GOA |
Gene Ontology Annotation |
http://www.ebi.ac.uk/GOA | |
| 939 |
GOPaD |
Gene Ontology Partition Database |
http://bcl.med.harvard.edu/proj/gopart | |
| 73 |
HGNC Database |
The HUGO Gene Nomenclature Database (formerly Genew) |
http://www.genenames.org/ | |
| 513 |
IUBMB Nomenclature database |
Nomenclature of enzymes, membrane transporters, electron transport proteins and other proteins |
http://www.chem.qmul.ac.uk/iubmb/ | |
| 514 |
IUPAC Nomenclature database |
Nomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commission |
http://www.chem.qmul.ac.uk/iupac/ | |
| 515 |
IUPHAR-RD |
International Union of Pharmacology recommendations on receptor nomenclature and drug classification |
http://www.iuphar-db.org/iuphar-rd/ | |
| 926 |
Plant Ontology DB |
Controlled vocabulary of plant structures and growth stages |
http://www.plantontology.org | |
| 358 |
SOURCE |
Functional genomics resource for human, mouse and rat |
http://source.stanford.edu | |
| 906 |
TreeBase |
Phylogenetic trees and the data matrices used to generate them |
http://www.treebase.org/ | |
| 317 |
UMLS |
Unified medical language system |
Requires user registration |
| 5.2. Taxonomy and identification |
| 1018 |
GeneTrees |
Pre-compiled alignments and gene phylogenies for a variety of taxonomic groups |
http://genetrees.vbi.vt.edu | |
| 78 |
ICB |
gyrB database for identification of bacteria |
http://seasquirt.mbio.co.jp/icb/ | |
| 1088 |
IDBD |
Infectious Disease Biomarker Database |
http://biomarker.korea.ac.kr | |
| 297 |
NCBI Taxonomy Browser |
Names of all organisms that are represented in GenBank |
http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html | |
| 299 |
RIDOM |
Ribosomal Differentiation of Medical Microorganisms |
http://www.ridom.de/ | |
| 1135 |
SuperCAT |
Database for multilocus sequence typing analysis of the Bacillus cereus group of bacteria |
http://mlstoslo.uio.no/ | |
| 301 |
Tree of Life |
Information on phylogeny and biodiversity |
http://phylogeny.arizona.edu/tree/phylogeny.html | |
| 965 |
VNTR Locus DB |
Bacterial Variable Number Tandem Repeat locus database |
http://vntr.csie.ntu.edu.tw/ | |
| 5.3. General genomics databases |
| 641 |
BacMap |
Picture atlas of annotated bacterial genomes |
http://wishart.biology.ualberta.ca/BacMap/ | |
| 650 |
CoGenT++ |
Complete genome tracking: Predicted peptides from fully sequenced genomes |
http://cgg.ebi.ac.uk/cgg/cpp_sitemap.html | |
| 445 |
DEG |
Database of Essential Genes |
http://tubic.tju.edu.cn/deg | |
| 1172 |
diArk |
Database of eukaryotic sequencing projects |
http://www.diark.org/diark/ | |
| 451 |
EBI Genomes |
EBI’s collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes |
http://www.ebi.ac.uk/genomes | |
| 458 |
Entrez Genomes |
NCBI’s collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Genome | |
| 461 |
ERGO-Light |
Integrated biochemical data on 10 bacterial genomes: Publicly-available portion of the ERGO database |
http://www.ergo-light.com/ | |
| 674 |
GenDiS |
Genomic distribution of protein structural superfamilies |
http://caps.ncbs.res.in/gendis/home.html | |
| 327 |
GeneNest |
Gene indices of human, mouse, zebrafish, etc. |
http://genenest.molgen.mpg.de/ | |
| 1077 |
GenoList |
An integrated environment for comparative analysis of microbial genomes |
http://genolist.pasteur.fr/ | |
| 484 |
Genome Information Broker |
DDBJ’s collection of genome databases |
http://gib.genes.nig.ac.jp | |
| 678 |
Genome Reviews |
Integrated view of complete genomes |
http://www.ebi.ac.uk/GenomeReviews/ | |
| 916 |
Genome Project DB |
NCBI's database of large-scale genome sequencing projects |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=genomeprj | |
| 75 |
GOLD |
Genomes online database: a listing of completed and ongoing genome projects |
http://www.genomesonline.org/ | |
| 830 |
HOINVGEN |
Homologous invertebrate genes |
http://pbil.univ-lyon1.fr/databases/hoinvgen/HOINVGEN.html | |
| 690 |
Inparanoid |
Database of eukaryotic orthologs |
http://inparanoid.cgb.ki.se/ | |
| 223 |
Integr8 |
Functional classification of proteins in whole genomes |
http://www.ebi.ac.uk/integr8/ | |
| 777 |
KaryotypeDB |
Karyotype and chromosome data for animal and plant species |
http://www.nenno.it/karyotypedb/ | |
| 112 |
KEGG |
Kyoto Encyclopedia of Genes and Genomes: databases on genes, proteins, and metabolic pathways |
http://www.genome.ad.jp/kegg | |
| 528 |
MBGD |
Microbial genome database for comparative analysis |
http://mbgd.genome.ad.jp/ | |
| 114 |
MetaCyc |
Metabolic pathways and enzymes from various organisms |
http://metacyc.org/ | |
| 1103 |
Narcisse |
Conserved syntenies for various animal, plant and bacterial genomes |
http://narcisse.toulouse.inra.fr | |
| 703 |
NegProt |
Negative Proteome: A tool for comparison of complete proteomes |
http://superfly.ucsd.edu/negprot | |
| 1040 |
NMPDR |
Database for functional annotation and comparative analysis of microbial genomes |
http://www.nmpdr.org | |
| 1106 |
OPTIC |
Orthologous and Paralogous Transcripts in Clades |
http://genserv.anat.ox.ac.uk/ | |
| 549 |
ORFanage |
Orphan ORFs (ORFs with no homologs) in microbial genomes |
No longer maintained |
| 1108 |
OrthoDB |
An hierarchical catalog of orthologous proteins in metazoa |
http://cegg.unige.ch/orthodb/browse | |
| 847 |
OrthoMCL |
Orthologous protein clusters from multiple genomes |
http://orthomcl.cbil.upenn.edu | |
| 715 |
PartiGeneDB |
Assembled partial genomes for ~250 eukaryotic organisms |
http://www.partigenedb.org/ | |
| 354 |
PEDANT |
Results of an automated analysis of genomic sequences |
http://pedant.gsf.de | |
| 377 |
PEP |
Predictions for Entire Proteomes |
http://cubic.bioc.columbia.edu/pep/ | |
| 1113 |
PhylomeDB |
Experimentally validated and predicted serine phosphorylation sites in Arabidopsis thaliana |
http://phylomedb.bioinfo.cipf.es | |
| 118 |
PUMA2 |
Metabolic analysis of complete microbial genomes |
http://compbio.mcs.anl.gov/puma2/ | |
| 582 |
STRING |
Predicted functional associations between proteins |
http://string.embl.de/ | |
| 66 |
TIGR Comprehensive Microbial Resource |
Various data on complete microbial genomes: Uniform annotation, properties of DNA and predicted proteins |
http://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl | |
| 5 |
TIGR Gene Indices |
Organism-specific databases of EST and gene sequences |
http://www.tigr.org/tdb/tgi.shtml | |
| 99 |
TIGR Microbial DB |
A list of microbial genome sequencing projects |
No longer maintained |
| 877 |
VBI Microbial Database |
Virginia Bioinformatics Institute microbial database |
http://phytophthora.vbi.vt.edu | |
| 5.4. Viral genome databases |
| 1051 |
BioHealthBase |
Host-pathogen interactions of influenza virus |
http://dev.biohealthbase.org/GSearch/PrototypeIndex.jsp | |
| 1061 |
CoVDB |
Database of coronavirus genes and genomes |
http://covdb.microbiology.hku.hk | |
| 810 |
DPVweb |
Descriptions of plant viruses |
http://www.dpvweb.net | |
| 1034 |
euHCVdb |
European Hepatitis C Virus database |
http://euhcvdb.ibcp.fr | |
| 492 |
HCV Database |
Hepatitis C Virus (HCV) Sequence Database |
http://hcv.lanl.gov/ | |
| 473 |
HCVdb |
Hepatitis C Virus Database |
http://hepatitis.ibcp.fr/ | |
| 972 |
HepSeq |
Epidemiological, clinical, and sequence data on the Hepatitis B virus |
http://www.hpa-bioinfodatabases.org.uk/ hepatitis_open/main.php | |
| 495 |
HERVd |
Human Endogenous Retrovirus database |
http://herv.img.cas.cz | |
| 497 |
HIV Drug Resistance Database |
HIV mutations that confer resistance to anti-HIV drugs |
http://resdb.lanl.gov/Resist_DB/default.htm | |
| 168 |
HIV Molecular Immunology Database |
HIV epitopes |
http://hiv-web.lanl.gov/immunology/ | |
| 990 |
HIV Positive Selection Mutation Database |
Positively selected mutations in HIV-1 protease and reverse transcriptase |
http://bioinfo.mbi.ucla.edu/HIV | |
| 909 |
Influenza Virus Resource |
Protein and nucleotide sequences of the influenza virus |
http://www.ncbi.nlm.nih.gov/genomes/FLU/FLU.html | |
| 993 |
IVDB |
Influenza Virus Database : Annotated sequences and geographic distribution of the influenza virus |
http://influenza.genomics.org.cn | |
| 602 |
NCBI Viral Genomes |
Viral genome resource at NCBI |
http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/viruses.html | |
| 725 |
Poxvirus.org |
Poxvirus genomic sequences and gene annotation |
http://www.poxvirus.org | |
| 750 |
T4-like genome DB |
Sequences of T4-like bacteriophages from various sources |
http://phage.bioc.tulane.edu | |
| 201 |
VIDA |
Homologous viral protein families database |
http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html | |
| 761 |
VIPERdb |
Virus particle explorer: Virus capsid structures |
http://viperdb.scripps.edu/ | |
| 798 |
Viral Bioinformatics Resource Center |
Virus orthologous genes, gene families and genomes |
http://www.biovirus.org | |
| 397 |
VirGen |
Curated database for complete viral genome sequences |
http://bioinfo.ernet.in/virgen/virgen.html | |
| 1039 |
ViTa |
microRNAs targets of the influenza virus |
http://vita.mbc.nctu.edu.tw | |
| 5.5. Prokaryotic genome databases |
| 5.5.1. General |
| 1044 |
AlterORF |
Database of alternate open reading frames |
http://www.cienciavida.cl/alterorf/ | |
| 641 |
BacMap |
Picture atlas of annotated bacterial genomes |
http://wishart.biology.ualberta.ca/BacMap | |
| 884 |
Comparative Genometrics |
DNA walks, nucleotide skews and other biometric measures of prokaryotic genomes |
http://www.unil.ch/comparativegenometrics/ | |
| 70 |
EMGlib |
Enhanced microbial genomes library: Completely sequenced genomes of unicellular organisms |
http://pbil.univ-lyon1.fr/emglib/emglib.html | |
| 328 |
GeneDB |
Curated database for various Sanger-sequenced genomes |
http://www.genedb.org/ | |
| 611 |
Genome Atlas |
DNA structural properties of sequenced genomes |
http://www.cbs.dtu.dk/services/GenomeAtlas/ | |
| 1084 |
HEG-DB |
Predicted highly expressed genes in prokaryotic genomes |
http://genomes.urv.cat/HEG-DB | |
| 352 |
HGT-DB |
Horizontal Gene Transfer-DataBase |
http://www.fut.es/~debb/HGT/ | |
| 828 |
IMG |
Comparative analysis of microbial genomes sequenced at the DOE Joint Genome Institute |
http://img.jgi.doe.gov/ | |
| 1089 |
IMG/M |
A data management and analysis system for metagenomes |
http://img.jgi.doe.gov/m | |
| 826 |
Interrupted coding sequences DB |
Interrupted coding sequences: frameshifts, stop codons, sequencing errors in microbial genomes |
http://www-bio3d-igbmc.u-strasbg.fr/ICDS/ | |
| 837 |
MeGX |
Marine ecological genomix: genomics and metagenomics of marine bacteria |
http://www.Megx.net | |
| 614 |
MetaGrowth |
Growth requirements of bacterial pathogens |
http://igs-server.cnrs-mrs.fr/axenic/ | |
| 959 |
MiST |
Microbial Signal Transduction database |
http://genomics.ornl.gov/mist/ | |
| 720 |
PGTdb |
Prokaryotic growth temperature database |
http://pgtdb.csie.ncu.edu.tw/ | |
| 43 |
RRNDB |
rRNA operon numbers in various prokaryotes |
http://rrndb.cme.msu.edu | |
| 1160 |
Roundup |
Repository of orthologs and corresponding evolutionary distances |
http://rodeo.med.harvard.edu/tools/roundup | |
| 866 |
SIDDBase |
Stress-induced DNA duplex destabilization profiles of complete microbial genomes |
http://www.genomecenter.ucdavis.edu/benham/siddbase/ | |
| 426 |
xBase |
A family of group-specific bacterial genome databases, includes coliBASE, CampyDB, ClostriDB, MycoDB, PseudoDB and others |
http://xbase.bham.ac.uk/ | |
| 5.5.2. Escherichia coli |
| 415 |
ASAP |
A Systematic Annotation Package |
https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm | |
| 428 |
CCDB |
CyberCell Database |
http://redpoll.pharmacy.ualberta.ca/CCDB | |
| 436 |
coliBase |
Database for E. coli, Salmonella and Shigella |
http://colibase.bham.ac.uk/ | |
| 437 |
Colibri |
http://genolist.pasteur.fr/Colibri/ | |
| 623 |
EchoBASE |
Post-genomic studies of Escherichia coli |
http://www.ecoli-york.org/ | |
| 108 |
EcoCyc |
E. coli K12 genes, pathways, transporters, and gene regulation |
http://ecocyc.org/ | |
| 69 |
EcoGene |
Sequence and literature data on E. coli genes and proteins |
http://ecogene.org/ | |
| 1070 |
ERIC |
Enteropathogen Resource Integration Center |
http://www.ericbrc.org | |
| 462 |
Essential genes in E. coli |
A list of genes essential for viability of E. coli |
http://www.genome.wisc.edu/resources/essential.htm | |
| 482 |
GenoBase |
Functional genomic aAnalysis of E. coli in Japan |
http://ecoli.aist-nara.ac.jp/ | |
| 165 |
GenProtEC |
E. coli K12 genome and proteome database |
http://genprotec.mbl.edu | |
