1. Nucleotide Sequence Databases 2. RNA sequence databases
3. Protein sequence databases 4. Structure Databases 5. Genomics Databases (non-human) 6. Metabolic Enzymes and Pathways; Signaling Pathways 7. Human and other Vertebrate Genomes 8. Human Genes and Diseases 9. Microarray Data and other Gene Expression Databases
10. Proteomics Resources
11. Other Molecular Biology Databases 12. Organelle Databases 13. Plant Databases 14. Immunological Databases

详细列表


Table 1. Molecular Biology Database Collectiona

No.b
 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. DNA sequences: genes, motifs and regulatory sites
1.2.1. Coding and coding DNA
403 ACLAME A classification of genetic mobile elements http://aclame.ulb.ac.be/
30 CUTG Codon usage tabulated from GenBank http://www.kazusa.or.jp/codon/
480 Genetic Codes Genetic codes in various organisms and organelles http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
668 Entrez Gene Gene-centered information at NCBI http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
495 HERVd Human endogenous retrovirus database http://herv.img.cas.cz
687 Hoppsigen Human and mouse homologous processed pseudogenes http://pbil.univ-lyon1.fr/databases/hoppsigen.html
294 Imprinted Gene Catalogue Imprinted genes and parent-of-origin effects in animals http://www.otago.ac.nz/IGC
512 Islander Pathogenicity islands and prophages in bacterial genomes http://www.indiana.edu/~islander
343 MICdb Prokaryotic microsatellites http://www.cdfd.org.in/micas
707 NPRD Nucleosome positioning region database http://srs6.bionet.nsc.ru/srs6/
47 STRBase Short tandem DNA repeats database http://www.cstl.nist.gov/div831/strbase/
5 TIGR Gene Indices Organism-specific databases of EST and gene sequences http://www.tigr.org/tdb/tgi.shtml
48 Transterm Codon usage, start and stop signals http://uther.otago.ac.nz/Transterm.html
6 UniGene Non-redundant set of eukaryotic gene-oriented clusters http://www.ncbi.nlm.nih.gov/UniGene/
320 UniVec Vector sequences, adapters, linkers and primers used in DNA cloning, can be used to check for vector contamination http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html
302 VectorDB Characterization and classification of nucleic acid vectors http://genome-www2.stanford.edu/vectordb/
305 Xpro Eukaryotic protein-encoding DNA sequences, both intron-containing and intron-less genes http://origin.bic.nus.edu.sg/xpro/
1.2.2. Gene structure, introns and exons, splice sites
414 ASAP Alternative spliced isoforms http://www.bioinformatics.ucla.edu/ASAP
28 ASD Alternative splicing database at EBI, includes three databases AltSplice, AltExtron and AEdb http://www.ebi.ac.uk/asd
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 database http://sege.ntu.edu.sg/wester/ashes/
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/
34 ExInt Exon–intron structure of eukaryotic genes http://sege.ntu.edu.sg/wester/exint/
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://www.cse.ucsc.edu/~kent/intronerator/
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://140.115.50.96/SpliceInfo/
580 SpliceNest A tool for visualizing splicing of genes from EST data http://splicenest.molgen.mpg.de/
1.2.3. Transcriptional regulator sites and transcription factors
231 ACTIVITY Functional DNA/RNA site activity http://wwwmgs.bionet.nsc.ru/mgs/systems/activity/
31 DBTBS Bacillus subtilis promoters and transcription factors http://dbtbs.hgc.jp/
663 DoOP Database 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
494 HemoPDB Hematopoietic promoter database: transcriptional regulation in hematopoiesis http://bioinformatics.med.ohio-state.edu/HemoPDB
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
40 PLACE Plant cis-acting regulatory DNA elements http://www.dna.affrc.go.jp/htdocs/PLACE
41 PlantCARE Plant promoters and cis-acting regulatory elements http://intra.psb.ugent.be:8080/PlantCARE/
563 PlantProm Plant promoter sequences for RNA polymerase II http://mendel.cs.rhul.ac.uk/
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://bioinfo.md.huji.ac.il/marg/promec
246 SELEX_DB DNA and RNA binding sites for various proteins, found by systematic evolution of ligands by exponential enrichment http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/
227 TESS Transcription element search system http://www.cbil.upenn.edu/tess
756 TRACTOR db Transcription factors in gamma-proteobacteria database http://www.tractor.lncc.br/
345 TRANSCompel Composite regulatory elements affecting gene transcription in eukaryotes http://www.gene-regulation.com/pub/databases.html#transcompel
340 TRANSFAC Transcription factors and binding sites http://transfac.gbf.de/TRANSFAC/index.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/
2. RNA sequence databases
229 16S and 23S rRNA Mutation Database 16S and 23S ribosomal RNA mutations http://www.fandm.edu/Departments/Biology/Databases/RNA.html
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 mRNA database http://rc.kfshrc.edu.sa/ared
378 Mobile group II introns A database of group II introns, self-splicing catalytic RNAs http://www.fp.ucalgary.ca/group2introns/
463 European rRNA database All complete or nearly complete rRNA sequences http://www.psb.ugent.be/rRNA/
490 GtRDB Genomic tRNA database http://rna.wustl.edu/GtRDB
236 Guide RNA Database RNA editing in various kinetoplastid species http://biosun.bio.tu-darmstadt.de/goringer/gRNA/gRNA.html
76 HIV Sequence Database HIV RNA sequences http://hiv-web.lanl.gov/
689 HuSiDa Human siRNA database http://itb1.biologie.hu-berlin.de/~nebulus/sirna/
237 HyPaLib Hybrid pattern library: structural elements in classes of RNA http://bibiserv.techfak.uni-bielefeld.de/HyPa/
379 IRESdb Internal ribosome entry site database http://ifr31w3.toulouse.inserm.fr/IRESdatabase/
529 microRNA Registry Database of microRNAs (small non-coding RNAs) http://www.sanger.ac.uk/Software/Rfam/mirna/
380 NCIR Non-canonical interactions in RNA structures http://prion.bchs.uh.edu/bp_type/
381 ncRNAs Database Non-coding RNAs with regulatory functions http://biobases.ibch.poznan.pl/ncRNA/
705 NONCODE A database of non-coding RNAs http://www.bioinfo.org.cn/NONCODE/index.htm
240 PLANTncRNAs Plant non-coding RNAs http://www.prl.msu.edu/PLANTncRNAs
564 Plant snoRNA DB snoRNA genes in plant species http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home
723 PolyA_DB A database of mammalian mRNA polyadenylation http://polya.umdnj.edu/polyadb/
242 PseudoBase Database of RNA pseudoknots http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html
382 Rfam Non-coding RNA families http://www.sanger.ac.uk/Software/Rfam/
244 RISSC Ribosomal internal spacer sequence collection http://ulises.umh.es/RISSC
630 RNAdb Mammalian non-coding RNA database http://ncrna.bioinformatics.com.au/
245 RNA Modification Database Naturally modified nucleosides in RNA http://medlib.med.utah.edu/RNAmods/
43 RRNDB rRNA operon numbers in various prokaryotes http://rrndb.cme.msu.edu/
629 siRNAdb siRNA database and search engine http://sirna.cgb.ki.se/
247 Small RNA Database Small RNAs from prokaryotes and eukaryotes http://mbcr.bcm.tmc.edu/smallRNA
248 SRPDB Signal recognition particle database http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html
754 SSU rRNA Modification Database Modified nucleosides in small subunit rRNA http://medstat.med.utah.edu/SSUmods/
383 Subviral RNA Database Viroids and viroid-like RNAs http://subviral.med.uottawa.ca/
249 tmRNA Website tmRNA sequences and alignments http://www.indiana.edu/~tmrna
250 tmRDB tmRNA database http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html
251 tRNA sequences tRNA viewer and sequence editor http://www.uni-bayreuth.de/departments/biochemie/trna/
252 UTRdb/UTRsite 5'- and 3'-UTRs of eukaryotic mRNAs http://bighost.area.ba.cnr.it/srs6/
3. Protein sequence databases
3.1. General sequence databases
163 EXProt Sequences of proteins with experimentally verified function http://www.cmbi.kun.nl/EXProt/
542 NCBI Protein database All protein sequences: translated from GenBank and imported from other protein databases http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein
714 PA-GOSUB Protein sequences from model organisms, GO assignment and subcellular localization http://www.cs.ualberta.ca/~bioinfo/PA/ProteomeIndex.html
194 PIR-PSD Protein information resource protein sequence database, has been merged into the UniProt knowledgebase http://pir.georgetown.edu/
370 PIR-NREF PIR's non-redundant reference protein database http://pir.georgetown.edu/pirwww/pirnref.shtml
565 PRF Protein research foundation database of peptides: sequences, literature and unnatural amino acids http://www.prf.or.jp/en
197 Swiss-Prot Now UniProt/Swiss-Prot: expertly curated protein sequence database, section of the UniProt knowledgebase http://www.expasy.org/sprot
198 TrEMBL Now UniProt/TrEMBL: computer-annotated translations of EMBL nucleotide sequence entries: section of the UniProt knowledgebase http://www.expasy.org/sprot
775 UniParc UniProt archive: a repository of all protein sequences, consisting only of unique identifiers and sequence http://www.uniprot.org/database/archive.shtml
318 UniProt Universal protein knowledgebase: merged data from Swiss-Prot, TrEMBL and PIR protein sequence databases http://www.uniprot.org/
776 UniRef UniProt non-redundant reference database: clustered sets of related sequences (including splice variants and isoforms) http://www.uniprot.org/database/nref.shtml
3.2. Protein properties
221 AAindex Physicochemical properties of amino acids http://www.genome.ad.jp/aaindex/
729 ProNIT Thermodynamic data on protein–nucleic acid interactions http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html
280 ProTherm Thermodynamic data for wild-type and mutant proteins http://gibk26.bse.kyutech.ac.jp/jouhou/protherm/protherm.html
772 TECRdb Thermodynamics of enzyme-catalyzed reactions http://xpdb.nist.gov/enzyme_thermodynamics/
3.3. Protein localization and targeting
444 DBSubLoc Database of protein subcellular localization http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html
375 NESbase Nuclear export signals database http://www.cbs.dtu.dk/databases/NESbase
376 NLSdb Nuclear localization signals http://cubic.bioc.columbia.edu/db/NLSdb/
704 NMPdb Nuclear matrix associated proteins database http://www.rostlab.org/db/NMPdb/
706 NOPdb Nucleolar proteome database http://www.lamondlab.com/NOPdb/
734 PSORTdb Protein subcellular localization in bacteria http://db.psort.org/
745 SPD Secreted protein database http://spd.cbi.pku.edu.cn
587 THGS Transmembrane helices in genome sequences http://pranag.physics.iisc.ernet.in/thgs/
589 TMPDB Experimentally characterized transmembrane topologies http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/
3.4. Protein sequence motifs and active sites
374 ASC Active sequence collection: biologically active peptides http://bioinformatica.isa.cnr.it/ASC/
203 Blocks Alignments of conserved regions in protein families http://blocks.fhcrc.org/
440 CSA Catalytic site atlas: active sites and catalytic residues in enzymes of known 3D structure http://www.ebi.ac.uk/thornton-srv/databases/CSA/
438 COMe Co-ordination of metals etc.: classification of bioinorganic proteins (metalloproteins and some other complex proteins) http://www.ebi.ac.uk/come
771 CopS Comprehensive peptide signature database http://203.195.151.46/copsv2/index.html
666 eBLOCKS Highly conserved protein sequence blocks http://fold.stanford.edu/eblocks/acsearch.html
206 eMOTIF Protein sequence motif determination and searches http://motif.stanford.edu/emotif
179 Metalloprotein Site Database Metal-binding sites in metalloproteins http://metallo.scripps.edu/
209 O-GlycBase O- and C-linked glycosylation sites in proteins http://www.cbs.dtu.dk/databases/OGLYCBASE/
717 PDBSite 3D structure of protein functional sites http://srs6.bionet.nsc.ru/srs6/
187 Phospho.ELM S/T/Y protein phosphorylation sites (formerly PhosphoBase) http://phospho.elm.eu.org/
193 PROMISE Prosthetic centers and metal ions in protein active sites http://metallo.scripps.edu/PROMISE
215 PROSITE Biologically significant protein patterns and profiles http://www.expasy.org/prosite
732 ProTeus Signature sequences at the protein N- and C-termini http://www.proteus.cs.huji.ac.il/
3.5. Protein domain databases; protein classification
622 ADDA A database of protein domain classification http://ekhidna.biocenter.helsinki.fi:8080/examples/servlets/adda/
204 CDD Conserved domain database, includes protein domains from Pfam, SMART, COG and KOG databases http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
205 CluSTr Clusters of Swiss-Prot+TrEMBL proteins http://www.ebi.ac.uk/clustr
671 FunShift Functional divergence between the subfamilies of a protein domain family http://funshift.cgb.ki.se/
200 Hits A database of protein domains and motifs http://hits.isb-sib.ch/
207 InterPro Integrated resource of protein families, domains and functional sites http://www.ebi.ac.uk/interpro
208 iProClass Integrated protein classification database http://pir.georgetown.edu/iproclass/
561 PIRSF Family/superfamily classification of whole proteins http://pir.georgetown.edu/pirsf/
212 PRINTS Hierarchical gene family fingerprints http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/
210 Pfam Protein families: multiple sequence alignments and profile hidden Markov models of protein domains http://www.sanger.ac.uk/Software/Pfam/
727 PRECISE Predicted and consensus interaction sites in enzymes http://precise.bu.edu/precisedb/
214 ProDom Protein domain families http://www.toulouse.inra.fr/prodom.html
216 ProtoMap Hierarchical classification of Swiss-Prot proteins http://protomap.cornell.edu/
567 ProtoNet Hierarchical clustering of Swiss-Prot proteins http://www.protonet.cs.huji.ac.il/
740 S4 Structure-based sequence alignments of SCOP superfamilies http://compbio.mds.qmw.ac.uk/~james/S4.shtml
217 SBASE Protein domain sequences and tools http://www.icgeb.org/sbase
218 SMART Simple modular architecture research tool: signalling, extracellular and chromatin-associated protein domains http://smart.embl-heidelberg.de/
219 SUPFAM Grouping of sequence families into superfamilies http://pauling.mbu.iisc.ernet.in/~supfam
220 SYSTERS Systematic re-searching and clustering of proteins http://systers.molgen.mpg.de/
199 TIGRFAMs TIGR protein families adapted for functional annotation http://www.tigr.org/TIGRFAMs
3.6. Databases of individual protein families
156 AARSDB Aminoacyl-tRNA synthetase database http://rose.man.poznan.pl/aars/index.html
308 ASPD Artificial selected proteins/peptides database http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/
158 BacTregulators Transcriptional regulators of AraC and TetR families http://www.bactregulators.org/
364 CSDBase Cold shock domain-containing proteins http://www.chemie.uni-marburg.de/~csdbase/
653 CuticleDB Structural proteins of Arthropod cuticle http://bioinformatics.biol.uoa.gr/cuticleDB
658 DCCP Database of copper-chelating proteins http://sdbi.sdut.edu.cn/DCCP/en/index.php
160 DExH/D Family Database DEAD-box, DEAH-box and DExH-box proteins http://www.helicase.net/dexhd/dbhome.htm
161 Endogenous GPCR List G protein-coupled receptors; expression in cell lines http://www.tumor-gene.org/GPCR/gpcr.html
162 ESTHER Esterases and other alpha/beta hydrolase enzymes http://www.ensam.inra.fr/esther
464 EyeSite Families of proteins functioning in the eye http://eyesite.cryst.bbk.ac.uk/
166 GPCRDB G protein-coupled receptors database http://www.gpcr.org/7tm/
679 gpDB G-proteins and their interaction with GPCRs http://bioinformatics.biol.uoa.gr/gpDB
167 Histone Database Histone fold sequences and structures http://research.nhgri.nih.gov/histones/
169 Homeobox Page Homeobox proteins, classification and evolution http://www.biosci.ki.se/groups/tbu/homeo.html
293 Hox-Pro Homeobox genes database http://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hox-pro00.html
170 Homeodomain Resource Homeodomain sequences, structures and related genetic and genomic information http://research.nhgri.nih.gov/homeodomain/
366 HORDE Human olfactory receptor data exploratorium http://bioinfo.weizmann.ac.il/HORDE/
174 InBase Inteins (protein splicing elements) database: properties, sequences, bibliography http://www.neb.com/neb/inteins.html
518 KinG—Kinases in Genomes S/T/Y-specific protein kinases encoded in complete genomes http://hodgkin.mbu.iisc.ernet.in/~king
519 Knottins Database of knottins—small proteins with an unusual ‘disulfide through disulfide’ knot http://knottin.cbs.cnrs.fr
176 LGICdb Ligand-gated ion channel subunit sequences database http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html
368 Lipase Engineering Database Sequence, structure and function of lipases and esterases http://www.led.uni-stuttgart.de/
524 LOX-DB Mammalian, invertebrate, plant and fungal lipoxygenases http://www.dkfz-heidelberg.de/spec/lox-db/
177 MEROPS Database of proteolytic enzymes (peptidases) http://merops.sanger.ac.uk/
369 NPD Nuclear protein database http://npd.hgu.mrc.ac.uk/
546 NucleaRDB Nuclear receptor superfamily http://www.receptors.org/NR/
182 Nuclear Receptor Resource Nuclear receptor superfamily http://nrr.georgetown.edu/NRR/nrrhome.htm
183 NUREBASE Nuclear hormone receptors database http://www.ens-lyon.fr/LBMC/laudet/nurebase.html
184 Olfactory Receptor Database Sequences for olfactory receptor-like molecules http://senselab.med.yale.edu/senselab/ordb/
185 ooTFD Object-oriented transcription factors database http://www.ifti.org/ootfd
188 PKR Protein kinase resource: sequences, enzymology, genetics and molecular and structural properties http://pkr.sdsc.edu/html/index.shtml
759 PLPMDB Pyridoxal-5'-phosphate dependent enzymes mutations http://www.studiofmp.com/plpmdb/
609 ProLysED A database of bacterial protease systems http://genome.ukm.my/prolyses/
192 Prolysis Proteases and natural and synthetic protease inhibitors http://delphi.phys.univ-tours.fr/Prolysis/
224 REBASE Restriction enzymes and associated methylases http://rebase.neb.com/rebase/rebase.html
195 Ribonuclease P Database RNase P sequences, alignments and structures http://www.mbio.ncsu.edu/RNaseP/home.html
573 RPG Ribosomal protein gene database http://ribosome.miyazaki-med.ac.jp/
575 RTKdb Receptor tyrosine kinase sequences http://pbil.univ-lyon1.fr/RTKdb/
309 S/MARt dB Nuclear scaffold/matrix attached regions http://smartdb.bioinf.med.uni-goettingen.de/
741 Scorpion Database of scorpion toxins http://research.i2r.a-star.edu.sg:8080/scorpion/
372 SDAP Structural database of allergenic proteins and food allergens http://fermi.utmb.edu/SDAP
196 SENTRA Sensory signal transduction proteins http://www-wit.mcs.anl.gov/sentra/
373 SEVENS 7-transmembrane helix receptors (G-protein-coupled) http://sevens.cbrc.jp/
248 SRPDB Proteins of the signal recognition particles http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html
314 TrSDB Transcription factor database http://ibb.uab.es/trsdb
399 VKCDB Voltage-gated potassium channel database http://vkcdb.biology.ualberta.ca/
202 Wnt Database Wnt proteins and phenotypes http://www.stanford.edu/~rnusse/wntwindow.html
4. Structure Databases
4.1. Small molecules
646 ChEBI Chemical entities of biological interest http://www.ebi.ac.uk/chebi/
261 CSD Cambridge structural database: crystal structure information for organic and metal-organic compounds http://www.ccdc.cam.ac.uk/prods/csd/csd.html
265 HIC-Up Hetero-compound Information Centre—Uppsala http://xray.bmc.uu.se/hicup
402 AANT Amino acid–nucleotide interaction database http://aant.icmb.utexas.edu/
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/
4.2. Carbohydrates
429 CCSD Complex carbohydrate structure database (CarbBank) http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm
652 CSS Carbohydrate structure suite: carbohydrate 3D structures derived from the PDB http://www.dkfz.de/spec/css/
486 Glycan Carbohydrate database, part of the KEGG system http://glycan.genome.ad.jp/
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.jonmaber.demon.co.uk/monosaccharide
300 SWEET-DB Annotated carbohydrate structure and substance information http://www.dkfz-heidelberg.de/spec2/sweetdb/
4.3. Nucleic acid structure
272 NDB Nucleic acid-containing structures http://ndbserver.rutgers.edu/
273 NTDB Thermodynamic data for nucleic acids http://ntdb.chem.cuhk.edu.hk/
387 RNABase RNA-containing structures from PDB and NDB http://www.rnabase.org/
283 SCOR Structural classification of RNA: RNA motifs by structure, function and tertiary interactions http://scor.lbl.gov/
4.4. Protein structure
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.stanford.edu/
288 BAliBASE A database for comparison of multiple sequence alignments http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html
257 BioMagResBank NMR spectroscopic data for proteins and nucleic acids http://www.bmrb.wisc.edu/
384 CADB Conformational angles in proteins database http://cluster.physics.iisc.ernet.in/cadb/
258 CATH Protein domain structures database http://www.biochem.ucl.ac.uk/bsm/cath_new
259 CE 3D protein structure alignments http://cl.sdsc.edu/ce.html
260 CKAAPs DB Structurally similar proteins with dissimilar sequences http://ckaap.sdsc.edu/
442 Dali Protein fold classification using the Dali search engine http://www.bioinfo.biocenter.helsinki.fi:8080/dali/
385 Decoys ‘R’ Us Computer-generated protein conformations http://dd.stanford.edu/
447 DisProt Database of Protein Disorder: proteins that lack fixed 3D structure in their native states http://divac.ist.temple.edu/disprot
448 DomIns Domain insertions in known protein structures http://stash.mrc-lmb.cam.ac.uk/DomIns
264 DSDBASE Native and modeled disulfide bonds in proteins http://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.html
386 DSMM Database of simulated molecular motions http://projects.villa-bosch.de/dbase/dsmm/
452 eF-site Electrostatic surface of Functional site: electrostatic potentials and hydrophobic properties of the active sites http://ef-site.protein.osaka-u.ac.jp/eF-site
674 GenDiS Genomic distribution of protein structural superfamilies http://caps.ncbs.res.in/gendis/home.html
472 Gene3D Precalculated structural assignments for whole genomes http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/
489 GTD Genomic threading database: structural annotations of complete proteomes http://bioinf.cs.ucl.ac.uk/GTD
322 GTOP Protein fold predictions from genome sequences http://spock.genes.nig.ac.jp/~genome/
360 Het-PDB Navi Hetero-atoms in protein structures http://daisy.nagahama-i-bio.ac.jp/golab/hetpdbnavi.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 Sequences and 3D structures of vertebrate immunoglobulins, T cell receptors and MHC proteins http://imgt3d.igh.cnrs.fr/
268 ISSD Integrated sequence–structure database http://www.protein.bio.msu.su/issd
269 LPFC Library of protein family core structures http://www-smi.stanford.edu/projects/helix/LPFC
270 MMDB NCBI's database of 3D structures, part of NCBI Entrez http://www.ncbi.nlm.nih.gov/Structure
456 E-MSD EBI's macromolecular structure database http://www.ebi.ac.uk/msd
331 ModBase Annotated comparative protein structure models http://alto.compbio.ucsf.edu/modbase-cgi/index.cgi
262 MolMovDB Database of macromolecular movements: descriptions of protein and macromolecular motions, including movies http://bioinfo.mbb.yale.edu/MolMovDB/
274 PALI Phylogeny and alignment of homologous protein structures http://pauling.mbu.iisc.ernet.in/~pali
275 PASS2 Structural motifs of protein superfamilies http://ncbs.res.in/~faculty/mini/campass/pass.html
557 PepConfDB A database of peptide conformations http://www.peptidome.org/products/list.htm
276 PDB Protein structure databank: all publicly available 3D structures of proteins and nucleic acids http://www.rcsb.org/pdb
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.biochem.ucl.ac.uk/bsm/pdbsum
619 PDB_TM Transmembrane proteins with known 3D structure http://www.enzim.hu/PDB_TM/
719 Protein Folding Database Experimental data on protein folding http://pfd.med.monash.edu.au
282 SCOP Structural classification of proteins http://scop.mrc-lmb.cam.ac.uk/scop
284 Sloop Classification of protein loops http://www-cryst.bioc.cam.ac.uk/~sloop/
583 Structure Superposition Database Pairwise superposition of TIM-barrel structures http://ssd.rbvi.ucsf.edu/
585 SWISS-MODEL Repository Database of annotated 3D protein structure models http://swissmodel.expasy.org/repository
285 SUPERFAMILY Assignments of proteins to structural superfamilies http://supfam.org/
584 SURFACE Surface residues and functions annotated, compared and evaluated: a database of protein surface patches http://cbm.bio.uniroma2.it/surface
764 TargetDB Target data from worldwide structural genomics projects http://targetdb.pdb.org/
401 3D-GENOMICS Structural annotations for complete proteomes http://www.sbg.bio.ic.ac.uk/3dgenomics
310 TOPS Topology of protein structures database http://www.tops.leeds.ac.uk
5. Genomics Databases (non-human)
5.1. Genome annotation terms, ontologies and nomenclature
73 Genew Human gene nomenclature: approved gene symbols http://www.gene.ucl.ac.uk/nomenclature
487 GO Gene ontology consortium database http://www.geneontology.org/
389 GOA EBI's gene ontology annotation project http://www.ebi.ac.uk/GOA
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 The International Union of Pharmacology recommendations on receptor nomenclature and drug classification http://www.iuphar-db.org/iuphar-rd/
552 PANTHER Gene products organized by biological function http://panther.celera.com/
317 UMLS Unified medical language system http://umlsks.nlm.nih.gov/
5.1.1. Taxonomy and Identification
78 ICB gyrB database for identification and classification of bacteria http://seasquirt.mbio.co.jp/icb/index.php
297 NCBI Taxonomy Names of all organisms represented in GenBank http://www.ncbi.nlm.nih.gov/Taxonomy/
608 PANDIT Protein and associated nucleotide domains with inferred trees http://www.ebi.ac.uk/goldman-srv/pandit/
299 RIDOM rRNA-based differentiation of medical microorganisms http://www.ridom-rdna.de/
243 RDP-II Ribosomal database project http://rdp.cme.msu.edu
301 Tree of Life Information on phylogeny and biodiversity http://phylogeny.arizona.edu/tree/phylogeny.html
5.2. General genomics databases
7 COG Clusters of orthologous groups of proteins http://www.ncbi.nlm.nih.gov/COG
650 COGENT Complete genome tracking: predicted peptides from fully sequenced genomes http://maine.ebi.ac.uk:8000/services/cogent/
337 CORG Comparative regulatory genomics: conserved non-coding sequence blocks http://corg.molgen.mpg.de/
445 DEG Database of essential genes from bacteria and yeast http://tubic.tju.edu.cn/deg
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
453 EGO Eukaryotic gene orthologs: orthologous DNA sequences in the TIGR gene indices http://www.tigr.org/tdb/tgi/ego/
70 EMGlib Enhanced microbial genomes library: completely sequenced genomes of unicellular organisms http://pbil.univ-lyon1.fr/emglib/emglib.html
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 ERGOLight Integrated biochemical data on nine bacterial genomes: publicly available portion of the ERGO database http://www.ergo-light.com/ERGO
470 FusionDB Database of bacterial and archaeal gene fusion events http://igs-server.cnrs-mrs.fr/FusionDB
611 Genome Atlas DNA structural properties of sequenced genomes http://www.cbs.dtu.dk/services/GenomeAtlas/
484 Genome Information Broker DDBJ's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes http://gib.genes.nig.ac.jp
678 Genome Reviews Integrated view of complete genomes http://www.ebi.ac.uk/GenomeReviews/
75 GOLD Genomes online database: a listing of completed and ongoing genome projects http://www.genomesonline.org/
352 HGT-DB Putative horizontally transferred genes in prokaryotic genomes http://www.fut.es/~debb/HGT/
223 Integr8 Functional classification of proteins in whole genomes http://www.ebi.ac.uk/integr8/
112 KEGG Kyoto encyclopedia of genes and genomes: integrated suite of databases on genes, proteins and metabolic pathways http://www.genome.jp/kegg
528 MBGD Microbial genome database for comparative analysis http://mbgd.genome.ad.jp/
549 ORFanage Database of orphan ORFs (ORFs with no homologs) in complete microbial genomes http://www.cs.bgu.ac.il/~nomsiew/ORFans
551 PACRAT Archaeal and bacterial intergenic sequence features http://www.biosci.ohio-tate.edu/~pacrat
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/
99 TIGR Microbial Database Lists of completed and ongoing genome projects with links to complete genome sequences http://www.tigr.org/tdb/mdb/mdbcomplete.html
66 TIGR Comprehensive Microbial Resource Various data on complete microbial genomes: uniform annotation, properties of DNA and predicted proteins http://www.tigr.org/CMR
311 TransportDB Predicted membrane transporters in complete genomes, classified according to the TC classification system http://www.membranetransport.org/
118 WIT3 What is there? Metabolic reconstruction for completely sequenced microbial genomes http://www-wit.mcs.anl.gov/wit3/
5.3. Organism-specific databases
5.3.1. Viruses
473 HCVDB The hepatitis C virus database http://hepatitis.ibcp.fr/
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/
365 HIV RT and Protease Sequence Database HIV reverse transcriptase and protease sequences http://hivdb.stanford.edu/
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 database 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 VIPER Virus particle explorer: virus capsid structures http://mmtsb.scripps.edu/viper
303 VirOligo Virus-specific oligonucleotides for PCR and hybridization http://viroligo.okstate.edu/
5.3.2. Prokaryotes
641 BacMap Picture atlas of annotated bacterial genomes http://wishart.biology.ualberta.ca/BacMap
614 MetaGrowth Growth requirements of bacterial pathogens http://igs-server.cnrs-mrs.fr/axenic/
720 PGTdb Prokaryotic growth temperature database http://pgtdb.csie.ncu.edu.tw/
5.3.2.1. Escherichia coli
415 ASAP A systematic annotation package for community analysis of E.coli and related genomes https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm
428 CyberCell database A collection of data on E.coli K12 intended for mathematical modeling to simulate the bacterial cell http://redpoll.pharmacy.ualberta.ca/CCDB
436 coliBase A database for E.coli, Salmonella and Shigella http://colibase.bham.ac.uk/
437 Colibri E.coli genome database at Institut Pasteur http://genolist.pasteur.fr/Colibri/
623 EchoBASE Post-genomic studies of Escherichia coli http://www.ecoli-york.org/
462 Essential genes in E.coli First results of an E.coli gene deletion project http://www.genome.wisc.edu/resources/essential.htm
482 GenoBase E.coli genome database at Nara Institute http://ecoli.aist-nara.ac.jp/
165 GenProtEC E.coli K12 genome and proteome database http://genprotec.mbl.edu
555 PEC Profiling of E.coli chromosome http://shigen.lab.nig.ac.jp/ecoli/pec
108 EcoCyc E.coli K12 genes, metabolic pathways, transporters and gene regulation http://ecocyc.org/
69 EcoGene Sequence and literature data on E.coli genes and proteins http://bmb.med.miami.edu/EcoGene/EcoWeb/
116 RegulonDB Transcriptional regulation and operon organization in E.coli http://www.cifn.unam.mx/Computational_Genomics/regulondb/
5.3.2.2. Bacillus subtilis
424 BSORF Bacillus subtilis genome database at Kyoto U. http://bacillus.genome.ad.jp/
89 NRSub Non-redundant Bacillus subtilis database at U. Lyon http://pbil.univ-lyon1.fr/nrsub/nrsub.html
96 SubtiList Bacillus subtilis genome database at Institut Pasteur http://genolist.pasteur.fr/SubtiList/
5.3.2.3. Other bacteria
420 BioCyc Pathway/genome databases for many bacteria http://biocyc.org/
426 CampyDB Database for Campylobacter genome analysis http://campy.bham.ac.uk/
433 ClostriDB Finished and unfinished genomes of Clostridium spp. http://clostri.bham.ac.uk/
648 CIDB Chlamydia Interactive Database: gene expression data http://www.it.deakin.edu.au/CIDB
68 CyanoBase Cyanobacterial genomes http://www.kazusa.or.jp/cyano
521 LeptoList Leptospira interrogans genome http://bioinfo.hku.hk/LeptoList
534 MolliGen Genomic data on mollicutes http://cbi.labri.fr/outils/molligen/
733 PseudoCAP Pseudomonas aeruginosa genome database and community annotation project http://www.pseudomonas.com/
94 RsGDB Rhodobacter sphaeroides genome http://www.hgsc.bcm.tmc.edu/projects/microbial/Rsphaeroides/
762 VirFact Bacterial virulence factors and pathogenicity islands http://virfact.burnham.org/
760 Virulence Factors Reference database for microbial virulence factors http://zdsys.chgb.org.cn/VFs/main.htm
5.3.3. Unicellular eukaryotes
409 ApiEST-DB EST sequences from various Apicomplexan parasites http://www.cbil.upenn.edu/paradbs-servlet
439 CryptoDB Cryptosporidium parvum genome database http://cryptodb.org/
662 Diatom EST Database ESTs from two diatom algae, Thalassiosira pseudonana and Phaeodactylum tricornutum http://avesthagen.sznbowler.com/
446 DictyBase Universal resource for Dictyostelium discoideum http://dictybase.org/
72 Full-Malaria Full-length cDNA library from erythrocytic-stage Plasmodium falciparum http://fullmal.ims.u-tokyo.ac.jp/
328 GeneDB Curated database for various Sanger-sequenced genomes http://www.genedb.org/
698 LumbriBASE ESTs of the earthworm Lumbricus rubellus http://www.earthworms.org/
91 PlasmoDB Plasmodium genome database http://plasmodb.org/
586 TcruziDB Trypanosoma cruzi genome database http://tcruzidb.org/
359 ToxoDB Toxoplasma gondii genome database http://toxodb.org/
5.3.4. Fungi
5.3.4.1. Yeasts
635 AGD Ashbya gossypii genome database http://agd.unibas.ch
617 CandidaDB Candida albicans genome database http://genolist.pasteur.fr/CandidaDB
645 Candida Genome Candida albicans genome database http://www.candidagenome.org/
441 CYGD MIPS Comprehensive yeast genome database http://mips.gsf.de/proj/yeast
483 Génolevures A comparison of S.cerevisiae and 14 other yeast species http://cbi.labri.fr/Genolevures
730 PROPHECY Profiling of phenotypic characteristics in yeast http://prophecy.lundberg.gu.se/
576 SCMD Saccharomyces cerevisiae morphological database: micrographs of budding yeast mutants http://yeast.gi.k.u-tokyo.ac.jp/
577 SCPD Saccharomyces cerevisiae promoter database http://cgsigma.cshl.org/jian
357 SGD Saccharomyces genome database http://www.yeastgenome.org/
25 TRIPLES Transposon-insertion phenotypes, localization and expression in Saccharomyces http://ygac.med.yale.edu/triples/
306 YDPM Yeast deletion project and mitochondria database http://www-deletion.stanford.edu/YDPM/YDPM_index.html
342 Yeast Intron Database Ares lab database of splicesomal introns in S.cerevisiae http://www.cse.ucsc.edu/research/compbio/yeast_introns.html
254 Yeast snoRNA Database Yeast small nucleolar RNAs http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html
307 yMGV Yeast microarray global viewer http://www.transcriptome.ens.fr/ymgv/
763 YRC PDR Yeast resource center public data repository http://www.yeastrc.org/pdr/
5.3.4.2. Other fungi
425 CADRE Central Aspergillus data repository http://www.cadre.man.ac.uk/
435 COGEME Phytopathogenic fungi and oomycete EST database http://cogeme.ex.ac.uk
533 MNCDB MIPS Neurospora crassa database http://mips.gsf.de/proj/neurospora/
708 OGD Oomycete Genomics Database: ESTs and annotation http://www.oomycete.net/
98 Phytophthora Functional Genomics Database ESTs and expression data from P.infestans and P.sojae http://www.pfgd.org/pfgd/
5.3.5. Invertebrates
5.3.5.1. Caenorhabditis elegans
430 C.elegans Project Genome sequencing data at the Sanger Institute http://www.sanger.ac.uk/Projects/C_elegans
238 Intronerator Introns and splicing in C.elegans and C.briggsae http://www.cse.ucsc.edu/~kent/intronerator/
570 RNAiDB RNAi phenotypic analysis of C.elegans genes http://www.rnai.org/
100 WILMA C.elegans annotation database http://www.came.sbg.ac.at/wilma/
304 WorfDB C.elegans ORFeome http://worfdb.dfci.harvard.edu/
51 WormBase Data repository for C.elegans and C.briggsae: curated genome annotation, genetic and physical maps, pathways http://www.wormbase.org/
5.3.5.2. Drosophila melanogaster
71 FlyBase Drosophila sequences and genomic information http://flybase.bio.indiana.edu/
767 FlyBrain Database of the Drosophila nervous system http://flybrain.neurobio.arizona.edu
670 FlyMine Integration of insect genomic and proteomic data http://www.flymine.org/
467 FlyTrap Drosophila mutants created using GFP protein trap strategy http://flytrap.med.yale.edu/
471 GadFly Genome annotation database of Drosophila http://www.fruitfly.org
677 GeniSys Enhancer- and promoter-inserted mutants of Drosophila http://genisys.kaist.ac.kr:8080/
774 DPDB Drosophila polymorphism database http://dpdb.uab.es/
449 Drosophila microarray project Data and tools for Drosophila gene expression studies http://www.flyarrays.com/fruitfly
509 InterActive Fly Drosophila genes and their roles in development http://sdb.bio.purdue.edu/fly/aimain/1aahome.htm
5.3.5.3. Other invertebrates
410 AppaDB A database on the nematode Pristionchus pacificus http://appadb.eb.tuebingen.mpg.de/
643 BeetleBase Genome database of the beetle Tribolium castaneum http://www.bioinformatics.ksu.edu/BeetleBase/
649 Ciliate IES-MDS Db Macro- and micronuclear genes in spirotrichous ciliates http://oxytricha.princeton.edu/dimorphism/database.htm
434 CnidBase Cnidarian evolution and gene expression database http://cnidbase.bu.edu/
543 Nematode.net Parasitic nematode sequencing project http://nematode.net/
544 NEMBASE Nematode sequence and functional data database http://www.nematodes.org/
726 PPNEMA Plant-parasitic nematode rRNAs http://bighost.area.ba.cnr.it/PPNEMA/
743 SilkDB Silkworm Bombyx mori ESTs, mutants, photographs http://www.ab.a.u-tokyo.ac.jp/genome/
744 SilkSatDb A microsatellite database of the silkworm Bombyx mori http://www.cdfd.org.in/silksatdb/
747 SpodoBase Genomics of the butterfly Spodoptera frugiperda http://bioweb.ensam.inra.fr/spodobase/
6. Metabolic Enzymes and Pathways; Signaling Pathways
6.1. Enzymes and Enzyme Nomenclature
421 BRENDA Enzyme names and biochemical properties http://www.brenda.uni-koeln.de
109 ENZYME Enzyme nomenclature and properties http://www.expasy.org/enzyme
459 Enzyme Nomenclature IUBMB Nomenclature Committee recommendations http://www.chem.qmw.ac.uk/iubmb/enzyme
613 EzCatDB Enzyme Catalytic Mechanism Database http://mbs.cbrc.jp/EzCatDB/
508 IntEnz Integrated enzyme database and enzyme nomenclature http://www.ebi.ac.uk/intenz
716 PDBrtf Representation of target families of enzymes in PDB http://cgl.imim.es/pdbrtf/
758 SCOPEC Mapping of catalytic function to domain structure http://www.enzome.com/databases/scopec.php
6.2. Metabolic Pathways
644 BioSilico Integrated access to various metabolic databases http://biosilico.kaist.ac.kr/
112 KEGG Pathway Metabolic and regulatory pathways in complete genomes http://www.genome.jp/kegg/pathway.html
114 MetaCyc Metabolic pathways and enzymes from various organisms http://metacyc.org
115 PathDB Biochemical pathways, compounds and metabolism