The Molecular Biology Database Collection: 2005 update
Nucl. Acids Res. 2005 33: D5-D24; doi:10.1093/nar/gki139
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Michael Y. Galperin The Molecular Biology Database Collection: 2005 update Nucl. Acids Res. 2005 33: D5-D24; doi:10.1093/nar/gki139 |
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| 1. Nucleotide Sequence Databases | |||
| 1.1. International Nucleotide Sequence Database Collaboration | |||
| DDBJ—DNA Data Bank of Japan | All known nucleotide and protein sequences | http://www.ddbj.nig.ac.jp | |
| EMBL Nucleotide Sequence Database | All known nucleotide and protein sequences | http://www.ebi.ac.uk/embl.html | |
| 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 | |||
| ACLAME | A classification of genetic mobile elements | http://aclame.ulb.ac.be/ | |
| CUTG | Codon usage tabulated from GenBank | http://www.kazusa.or.jp/codon/ | |
| Genetic Codes | Genetic codes in various organisms and organelles | http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi | |
| Entrez Gene | Gene-centered information at NCBI | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene | |
| HERVd | Human endogenous retrovirus database | http://herv.img.cas.cz | |
| Hoppsigen | Human and mouse homologous processed pseudogenes | http://pbil.univ-lyon1.fr/databases/hoppsigen.html | |
| Imprinted Gene Catalogue | Imprinted genes and parent-of-origin effects in animals | http://www.otago.ac.nz/IGC | |
| Islander | Pathogenicity islands and prophages in bacterial genomes | http://www.indiana.edu/~islander | |
| MICdb | Prokaryotic microsatellites | http://www.cdfd.org.in/micas | |
| NPRD | Nucleosome positioning region database | http://srs6.bionet.nsc.ru/srs6/ | |
| STRBase | Short tandem DNA repeats database | http://www.cstl.nist.gov/div831/strbase/ | |
| TIGR Gene Indices | Organism-specific databases of EST and gene sequences | http://www.tigr.org/tdb/tgi.shtml | |
| Transterm | Codon usage, start and stop signals | http://uther.otago.ac.nz/Transterm.html | |
| UniGene | Non-redundant set of eukaryotic gene-oriented clusters | http://www.ncbi.nlm.nih.gov/UniGene/ | |
| 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 | |
| VectorDB | Characterization and classification of nucleic acid vectors | http://genome-www2.stanford.edu/vectordb/ | |
| 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 | |||
| ASAP | Alternative spliced isoforms | http://www.bioinformatics.ucla.edu/ASAP | |
| ASD | Alternative splicing database at EBI, includes three databases AltSplice, AltExtron and AEdb | http://www.ebi.ac.uk/asd | |
| ASDB | Alternative splicing database: protein products and expression patterns of alternatively spliced genes | http://hazelton.lbl.gov/~teplitski/alt | |
| ASHESdb | Alternatively spliced human genes by exon skipping database | http://sege.ntu.edu.sg/wester/ashes/ | |
| EASED | Extended alternatively spliced EST database | http://eased.bioinf.mdc-berlin.de/ | |
| ECgene | Genome annotation for alternative splicing | http://genome.ewha.ac.kr/ECgene/ | |
| EDAS | EST-derived alternative splicing database | http://www.ig-msk.ru:8005/EDAS/ | |
| ExInt | Exon–intron structure of eukaryotic genes | http://sege.ntu.edu.sg/wester/exint/ | |
| HS3D | Homo sapiens splice sites dataset | http://www.sci.unisannio.it/docenti/rampone/ | |
| Intronerator | Alternative splicing in C.elegans and C.briggsae | http://www.cse.ucsc.edu/~kent/intronerator/ | |
| SpliceDB | Canonical and non-canonical mammalian splice sites | http://www.softberry.com/berry.phtml?topic=splicedb&group=data&subgroup=spldb | |
| SpliceInfo | Modes of alternative splicing in human genome | http://140.115.50.96/SpliceInfo/ | |
| 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 | |||
| ACTIVITY | Functional DNA/RNA site activity | http://wwwmgs.bionet.nsc.ru/mgs/systems/activity/ | |
| DBTBS | Bacillus subtilis promoters and transcription factors | http://dbtbs.hgc.jp/ | |
| DoOP | Database of orthologous promoters: chordates and plants | http://doop.abc.hu/ | |
| DPInteract | Binding sites for E.coli DNA-binding proteins | http://arep.med.harvard.edu/dpinteract | |
| EPD | Eukaryotic promoter database | http://www.epd.isb-sib.ch | |
| HemoPDB | Hematopoietic promoter database: transcriptional regulation in hematopoiesis | http://bioinformatics.med.ohio-state.edu/HemoPDB | |
| JASPAR | PSSMs for transcription factor DNA-binding sites | http://jaspar.cgb.ki.se | |
| MAPPER | Putative transcription factor binding sites in various genomes | http://bio.chip.org/mapper | |
| PLACE | Plant cis-acting regulatory DNA elements | http://www.dna.affrc.go.jp/htdocs/PLACE | |
| PlantCARE | Plant promoters and cis-acting regulatory elements | http://intra.psb.ugent.be:8080/PlantCARE/ | |
| PlantProm | Plant promoter sequences for RNA polymerase II | http://mendel.cs.rhul.ac.uk/ | |
| PRODORIC | Prokaryotic database of gene regulation networks | http://prodoric.tu-bs.de/ | |
| PromEC | E.coli promoters with experimentally identified transcriptional start sites | http://bioinfo.md.huji.ac.il/marg/promec | |
| 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/ | |
| TESS | Transcription element search system | http://www.cbil.upenn.edu/tess | |
| TRACTOR db | Transcription factors in gamma-proteobacteria database | http://www.tractor.lncc.br/ | |
| TRANSCompel | Composite regulatory elements affecting gene transcription in eukaryotes | http://www.gene-regulation.com/pub/databases.html#transcompel | |
| TRANSFAC | Transcription factors and binding sites | http://transfac.gbf.de/TRANSFAC/index.html | |
| TRED | Transcriptional regulatory element database | http://rulai.cshl.edu/tred | |
| TRRD | Transcription regulatory regions of eukaryotic genes | http://www.bionet.nsc.ru/trrd/ | |
| 2. RNA sequence databases | |||
| 16S and 23S rRNA Mutation Database | 16S and 23S ribosomal RNA mutations | http://www.fandm.edu/Departments/Biology/Databases/RNA.html | |
| 5S rRNA Database | 5S rRNA sequences | http://biobases.ibch.poznan.pl/5SData/ | |
| Aptamer database | Small RNA/DNA molecules binding nucleic acids, proteins | http://aptamer.icmb.utexas.edu/ | |
| ARED | AU-rich element-containing mRNA database | http://rc.kfshrc.edu.sa/ared | |
| Mobile group II introns | A database of group II introns, self-splicing catalytic RNAs | http://www.fp.ucalgary.ca/group2introns/ | |
| European rRNA database | All complete or nearly complete rRNA sequences | http://www.psb.ugent.be/rRNA/ | |
| GtRDB | Genomic tRNA database | http://rna.wustl.edu/GtRDB | |
| Guide RNA Database | RNA editing in various kinetoplastid species | http://biosun.bio.tu-darmstadt.de/goringer/gRNA/gRNA.html | |
| HIV Sequence Database | HIV RNA sequences | http://hiv-web.lanl.gov/ | |
| HuSiDa | Human siRNA database | http://itb1.biologie.hu-berlin.de/~nebulus/sirna/ | |
| HyPaLib | Hybrid pattern library: structural elements in classes of RNA | http://bibiserv.techfak.uni-bielefeld.de/HyPa/ | |
| IRESdb | Internal ribosome entry site database | http://ifr31w3.toulouse.inserm.fr/IRESdatabase/ | |
| microRNA Registry | Database of microRNAs (small non-coding RNAs) | http://www.sanger.ac.uk/Software/Rfam/mirna/ | |
| NCIR | Non-canonical interactions in RNA structures | http://prion.bchs.uh.edu/bp_type/ | |
| ncRNAs Database | Non-coding RNAs with regulatory functions | http://biobases.ibch.poznan.pl/ncRNA/ | |
| NONCODE | A database of non-coding RNAs | http://www.bioinfo.org.cn/NONCODE/index.htm | |
| PLANTncRNAs | Plant non-coding RNAs | http://www.prl.msu.edu/PLANTncRNAs | |
| Plant snoRNA DB | snoRNA genes in plant species | http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home | |
| PolyA_DB | A database of mammalian mRNA polyadenylation | http://polya.umdnj.edu/polyadb/ | |
| PseudoBase | Database of RNA pseudoknots | http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html | |
| Rfam | Non-coding RNA families | http://www.sanger.ac.uk/Software/Rfam/ | |
| RISSC | Ribosomal internal spacer sequence collection | http://ulises.umh.es/RISSC | |
| RNAdb | Mammalian non-coding RNA database | http://ncrna.bioinformatics.com.au/ | |
| RNA Modification Database | Naturally modified nucleosides in RNA | http://medlib.med.utah.edu/RNAmods/ | |
| RRNDB | rRNA operon numbers in various prokaryotes | http://rrndb.cme.msu.edu/ | |
| siRNAdb | siRNA database and search engine | http://sirna.cgb.ki.se/ | |
| Small RNA Database | Small RNAs from prokaryotes and eukaryotes | http://mbcr.bcm.tmc.edu/smallRNA | |
| SRPDB | Signal recognition particle database | http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html | |
| SSU rRNA Modification Database | Modified nucleosides in small subunit rRNA | http://medstat.med.utah.edu/SSUmods/ | |
| Subviral RNA Database | Viroids and viroid-like RNAs | http://subviral.med.uottawa.ca/ | |
| tmRNA Website | tmRNA sequences and alignments | http://www.indiana.edu/~tmrna | |
| tmRDB | tmRNA database | http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html | |
| tRNA sequences | tRNA viewer and sequence editor | http://www.uni-bayreuth.de/departments/biochemie/trna/ | |
| 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 | |||
| EXProt | Sequences of proteins with experimentally verified function | http://www.cmbi.kun.nl/EXProt/ | |
| NCBI Protein database | All protein sequences: translated from GenBank and imported from other protein databases | http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Protein | |
| PA-GOSUB | Protein sequences from model organisms, GO assignment and subcellular localization | http://www.cs.ualberta.ca/~bioinfo/PA/ProteomeIndex.html | |
| PIR-PSD | Protein information resource protein sequence database, has been merged into the UniProt knowledgebase | http://pir.georgetown.edu/ | |
| PIR-NREF | PIR's non-redundant reference protein database | http://pir.georgetown.edu/pirwww/pirnref.shtml | |
| PRF | Protein research foundation database of peptides: sequences, literature and unnatural amino acids | http://www.prf.or.jp/en | |
| Swiss-Prot | Now UniProt/Swiss-Prot: expertly curated protein sequence database, section of the UniProt knowledgebase | http://www.expasy.org/sprot | |
| TrEMBL | Now UniProt/TrEMBL: computer-annotated translations of EMBL nucleotide sequence entries: section of the UniProt knowledgebase | http://www.expasy.org/sprot | |
| UniParc | UniProt archive: a repository of all protein sequences, consisting only of unique identifiers and sequence | http://www.uniprot.org/database/archive.shtml | |
| UniProt | Universal protein knowledgebase: merged data from Swiss-Prot, TrEMBL and PIR protein sequence databases | http://www.uniprot.org/ | |
| 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 | |||
| AAindex | Physicochemical properties of amino acids | http://www.genome.ad.jp/aaindex/ | |
| ProNIT | Thermodynamic data on protein–nucleic acid interactions | http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html | |
| ProTherm | Thermodynamic data for wild-type and mutant proteins | http://gibk26.bse.kyutech.ac.jp/jouhou/protherm/protherm.html | |
| TECRdb | Thermodynamics of enzyme-catalyzed reactions | http://xpdb.nist.gov/enzyme_thermodynamics/ | |
| 3.3. Protein localization and targeting | |||
| DBSubLoc | Database of protein subcellular localization | http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html | |
| NESbase | Nuclear export signals database | http://www.cbs.dtu.dk/databases/NESbase | |
| NLSdb | Nuclear localization signals | http://cubic.bioc.columbia.edu/db/NLSdb/ | |
| NMPdb | Nuclear matrix associated proteins database | http://www.rostlab.org/db/NMPdb/ | |
| NOPdb | Nucleolar proteome database | http://www.lamondlab.com/NOPdb/ | |
| PSORTdb | Protein subcellular localization in bacteria | http://db.psort.org/ | |
| SPD | Secreted protein database | http://spd.cbi.pku.edu.cn | |
| THGS | Transmembrane helices in genome sequences | http://pranag.physics.iisc.ernet.in/thgs/ | |
| TMPDB | Experimentally characterized transmembrane topologies | http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/ | |
| 3.4. Protein sequence motifs and active sites | |||
| ASC | Active sequence collection: biologically active peptides | http://bioinformatica.isa.cnr.it/ASC/ | |
| Blocks | Alignments of conserved regions in protein families | http://blocks.fhcrc.org/ | |
| CSA | Catalytic site atlas: active sites and catalytic residues in enzymes of known 3D structure | http://www.ebi.ac.uk/thornton-srv/databases/CSA/ | |
| COMe | Co-ordination of metals etc.: classification of bioinorganic proteins (metalloproteins and some other complex proteins) | http://www.ebi.ac.uk/come | |
| CopS | Comprehensive peptide signature database | http://203.195.151.46/copsv2/index.html | |
| eBLOCKS | Highly conserved protein sequence blocks | http://fold.stanford.edu/eblocks/acsearch.html | |
| eMOTIF | Protein sequence motif determination and searches | http://motif.stanford.edu/emotif | |
| Metalloprotein Site Database | Metal-binding sites in metalloproteins | http://metallo.scripps.edu/ | |
| O-GlycBase | O- and C-linked glycosylation sites in proteins | http://www.cbs.dtu.dk/databases/OGLYCBASE/ | |
| PDBSite | 3D structure of protein functional sites | http://srs6.bionet.nsc.ru/srs6/ | |
| Phospho.ELM | S/T/Y protein phosphorylation sites (formerly PhosphoBase) | http://phospho.elm.eu.org/ | |
| PROMISE | Prosthetic centers and metal ions in protein active sites | http://metallo.scripps.edu/PROMISE | |
| PROSITE | Biologically significant protein patterns and profiles | http://www.expasy.org/prosite | |
| ProTeus | Signature sequences at the protein N- and C-termini | http://www.proteus.cs.huji.ac.il/ | |
| 3.5. Protein domain databases; protein classification | |||
| ADDA | A database of protein domain classification | http://ekhidna.biocenter.helsinki.fi:8080/examples/servlets/adda/ | |
| CDD | Conserved domain database, includes protein domains from Pfam, SMART, COG and KOG databases | http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml | |
| CluSTr | Clusters of Swiss-Prot+TrEMBL proteins | http://www.ebi.ac.uk/clustr | |
| FunShift | Functional divergence between the subfamilies of a protein domain family | http://funshift.cgb.ki.se/ | |
| Hits | A database of protein domains and motifs | http://hits.isb-sib.ch/ | |
| InterPro | Integrated resource of protein families, domains and functional sites | http://www.ebi.ac.uk/interpro | |
| iProClass | Integrated protein classification database | http://pir.georgetown.edu/iproclass/ | |
| PIRSF | Family/superfamily classification of whole proteins | http://pir.georgetown.edu/pirsf/ | |
| PRINTS | Hierarchical gene family fingerprints | http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/ | |
| Pfam | Protein families: multiple sequence alignments and profile hidden Markov models of protein domains | http://www.sanger.ac.uk/Software/Pfam/ | |
| PRECISE | Predicted and consensus interaction sites in enzymes | http://precise.bu.edu/precisedb/ | |
| ProDom | Protein domain families | http://www.toulouse.inra.fr/prodom.html | |
| ProtoMap | Hierarchical classification of Swiss-Prot proteins | http://protomap.cornell.edu/ | |
| ProtoNet | Hierarchical clustering of Swiss-Prot proteins | http://www.protonet.cs.huji.ac.il/ | |
| S4 | Structure-based sequence alignments of SCOP superfamilies | http://compbio.mds.qmw.ac.uk/~james/S4.shtml | |
| SBASE | Protein domain sequences and tools | http://www.icgeb.org/sbase | |
| SMART | Simple modular architecture research tool: signalling, extracellular and chromatin-associated protein domains | http://smart.embl-heidelberg.de/ | |
| SUPFAM | Grouping of sequence families into superfamilies | http://pauling.mbu.iisc.ernet.in/~supfam | |
| SYSTERS | Systematic re-searching and clustering of proteins | http://systers.molgen.mpg.de/ | |
| TIGRFAMs | TIGR protein families adapted for functional annotation | http://www.tigr.org/TIGRFAMs | |
| 3.6. Databases of individual protein families | |||
| AARSDB | Aminoacyl-tRNA synthetase database | http://rose.man.poznan.pl/aars/index.html | |
| ASPD | Artificial selected proteins/peptides database | http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/ | |
| BacTregulators | Transcriptional regulators of AraC and TetR families | http://www.bactregulators.org/ | |
| CSDBase | Cold shock domain-containing proteins | http://www.chemie.uni-marburg.de/~csdbase/ | |
| CuticleDB | Structural proteins of Arthropod cuticle | http://bioinformatics.biol.uoa.gr/cuticleDB | |
| DCCP | Database of copper-chelating proteins | http://sdbi.sdut.edu.cn/DCCP/en/index.php | |
| DExH/D Family Database | DEAD-box, DEAH-box and DExH-box proteins | http://www.helicase.net/dexhd/dbhome.htm | |
| Endogenous GPCR List | G protein-coupled receptors; expression in cell lines | http://www.tumor-gene.org/GPCR/gpcr.html | |
| ESTHER | Esterases and other alpha/beta hydrolase enzymes | http://www.ensam.inra.fr/esther | |
| EyeSite | Families of proteins functioning in the eye | http://eyesite.cryst.bbk.ac.uk/ | |
| GPCRDB | G protein-coupled receptors database | http://www.gpcr.org/7tm/ | |
| gpDB | G-proteins and their interaction with GPCRs | http://bioinformatics.biol.uoa.gr/gpDB | |
| Histone Database | Histone fold sequences and structures | http://research.nhgri.nih.gov/histones/ | |
| Homeobox Page | Homeobox proteins, classification and evolution | http://www.biosci.ki.se/groups/tbu/homeo.html | |
| Hox-Pro | Homeobox genes database | http://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hox-pro00.html | |
| Homeodomain Resource | Homeodomain sequences, structures and related genetic and genomic information | http://research.nhgri.nih.gov/homeodomain/ | |
| HORDE | Human olfactory receptor data exploratorium | http://bioinfo.weizmann.ac.il/HORDE/ | |
| InBase | Inteins (protein splicing elements) database: properties, sequences, bibliography | http://www.neb.com/neb/inteins.html | |
| KinG—Kinases in Genomes | S/T/Y-specific protein kinases encoded in complete genomes | http://hodgkin.mbu.iisc.ernet.in/~king | |
| Knottins | Database of knottins—small proteins with an unusual ‘disulfide through disulfide’ knot | http://knottin.cbs.cnrs.fr | |
| LGICdb | Ligand-gated ion channel subunit sequences database | http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html | |
| Lipase Engineering Database | Sequence, structure and function of lipases and esterases | http://www.led.uni-stuttgart.de/ | |
| LOX-DB | Mammalian, invertebrate, plant and fungal lipoxygenases | http://www.dkfz-heidelberg.de/spec/lox-db/ | |
| MEROPS | Database of proteolytic enzymes (peptidases) | http://merops.sanger.ac.uk/ | |
| NPD | Nuclear protein database | http://npd.hgu.mrc.ac.uk/ | |
| NucleaRDB | Nuclear receptor superfamily | http://www.receptors.org/NR/ | |
| Nuclear Receptor Resource | Nuclear receptor superfamily | http://nrr.georgetown.edu/NRR/nrrhome.htm | |
| NUREBASE | Nuclear hormone receptors database | http://www.ens-lyon.fr/LBMC/laudet/nurebase.html | |
| Olfactory Receptor Database | Sequences for olfactory receptor-like molecules | http://senselab.med.yale.edu/senselab/ordb/ | |
| ooTFD | Object-oriented transcription factors database | http://www.ifti.org/ootfd | |
| PKR | Protein kinase resource: sequences, enzymology, genetics and molecular and structural properties | http://pkr.sdsc.edu/html/index.shtml | |
| PLPMDB | Pyridoxal-5'-phosphate dependent enzymes mutations | http://www.studiofmp.com/plpmdb/ | |
| ProLysED | A database of bacterial protease systems | http://genome.ukm.my/prolyses/ | |
| Prolysis | Proteases and natural and synthetic protease inhibitors | http://delphi.phys.univ-tours.fr/Prolysis/ | |
| REBASE | Restriction enzymes and associated methylases | http://rebase.neb.com/rebase/rebase.html | |
| Ribonuclease P Database | RNase P sequences, alignments and structures | http://www.mbio.ncsu.edu/RNaseP/home.html | |
| RPG | Ribosomal protein gene database | http://ribosome.miyazaki-med.ac.jp/ | |
| RTKdb | Receptor tyrosine kinase sequences | http://pbil.univ-lyon1.fr/RTKdb/ | |
| S/MARt dB | Nuclear scaffold/matrix attached regions | http://smartdb.bioinf.med.uni-goettingen.de/ | |
| Scorpion | Database of scorpion toxins | http://research.i2r.a-star.edu.sg:8080/scorpion/ | |
| SDAP | Structural database of allergenic proteins and food allergens | http://fermi.utmb.edu/SDAP | |
| SENTRA | Sensory signal transduction proteins | http://www-wit.mcs.anl.gov/sentra/ | |
| SEVENS | 7-transmembrane helix receptors (G-protein-coupled) | http://sevens.cbrc.jp/ | |
| SRPDB | Proteins of the signal recognition particles | http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html | |
| TrSDB | Transcription factor database | http://ibb.uab.es/trsdb | |
| VKCDB | Voltage-gated potassium channel database | http://vkcdb.biology.ualberta.ca/ | |
| Wnt Database | Wnt proteins and phenotypes | http://www.stanford.edu/~rnusse/wntwindow.html | |
| 4. Structure Databases | |||
| 4.1. Small molecules | |||
| ChEBI | Chemical entities of biological interest | http://www.ebi.ac.uk/chebi/ | |
| CSD | Cambridge structural database: crystal structure information for organic and metal-organic compounds | http://www.ccdc.cam.ac.uk/prods/csd/csd.html | |
| HIC-Up | Hetero-compound Information Centre—Uppsala | http://xray.bmc.uu.se/hicup | |
| AANT | Amino acid–nucleotide interaction database | http://aant.icmb.utexas.edu/ | |
| Klotho | Collection and categorization of biological compounds | http://www.biocheminfo.org/klotho | |
| LIGAND | Chemical compounds and reactions in biological pathways | http://www.genome.ad.jp/ligand/ | |
| PDB-Ligand | 3D structures of small molecules bound to proteins and nucleic acids | http://www.idrtech.com/PDB-Ligand/ | |
| PubChem | Structures and biological activities of small organic molecules | http://pubchem.ncbi.nlm.nih.gov/ | |
| 4.2. Carbohydrates | |||
| CCSD | Complex carbohydrate structure database (CarbBank) | http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm | |
| CSS | Carbohydrate structure suite: carbohydrate 3D structures derived from the PDB | http://www.dkfz.de/spec/css/ | |
| Glycan | Carbohydrate database, part of the KEGG system | http://glycan.genome.ad.jp/ | |
| GlycoSuiteDB | N- and O-linked glycan structures and biological sources | http://www.glycosuite.com/ | |
| Monosaccharide Browser | Space-filling Fischer projections of monosaccharides | http://www.jonmaber.demon.co.uk/monosaccharide | |
| SWEET-DB | Annotated carbohydrate structure and substance information | http://www.dkfz-heidelberg.de/spec2/sweetdb/ | |
| 4.3. Nucleic acid structure | |||
| NDB | Nucleic acid-containing structures | http://ndbserver.rutgers.edu/ | |
| NTDB | Thermodynamic data for nucleic acids | http://ntdb.chem.cuhk.edu.hk/ | |
| RNABase | RNA-containing structures from PDB and NDB | http://www.rnabase.org/ | |
| SCOR | Structural classification of RNA: RNA motifs by structure, function and tertiary interactions | http://scor.lbl.gov/ | |
| 4.4. Protein structure | |||
| ArchDB | Automated classification of protein loop structures | http://gurion.imim.es/archdb | |
| ASTRAL | Sequences of domains of known structure, selected subsets and sequence–structure correspondences | http://astral.stanford.edu/ | |
| BAliBASE | A database for comparison of multiple sequence alignments | http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html | |
| BioMagResBank | NMR spectroscopic data for proteins and nucleic acids | http://www.bmrb.wisc.edu/ | |
| CADB | Conformational angles in proteins database | http://cluster.physics.iisc.ernet.in/cadb/ | |
| CATH | Protein domain structures database | http://www.biochem.ucl.ac.uk/bsm/cath_new | |
| CE | 3D protein structure alignments | http://cl.sdsc.edu/ce.html | |
| CKAAPs DB | Structurally similar proteins with dissimilar sequences | http://ckaap.sdsc.edu/ | |
| Dali | Protein fold classification using the Dali search engine | http://www.bioinfo.biocenter.helsinki.fi:8080/dali/ | |
| Decoys ‘R’ Us | Computer-generated protein conformations | http://dd.stanford.edu/ | |
| DisProt | Database of Protein Disorder: proteins that lack fixed 3D structure in their native states | http://divac.ist.temple.edu/disprot | |
| DomIns | Domain insertions in known protein structures | http://stash.mrc-lmb.cam.ac.uk/DomIns | |
| DSDBASE | Native and modeled disulfide bonds in proteins | http://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.html | |
| DSMM | Database of simulated molecular motions | http://projects.villa-bosch.de/dbase/dsmm/ | |
| 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 | |
| GenDiS | Genomic distribution of protein structural superfamilies | http://caps.ncbs.res.in/gendis/home.html | |
| Gene3D | Precalculated structural assignments for whole genomes | http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/ | |
| GTD | Genomic threading database: structural annotations of complete proteomes | http://bioinf.cs.ucl.ac.uk/GTD | |
| GTOP | Protein fold predictions from genome sequences | http://spock.genes.nig.ac.jp/~genome/ | |
| Het-PDB Navi | Hetero-atoms in protein structures | http://daisy.nagahama-i-bio.ac.jp/golab/hetpdbnavi.html | |
| HOMSTRAD | Homologous structure alignment database: curated structure-based alignments for protein families | http://www-cryst.bioc.cam.ac.uk/homstrad | |
| IMB Jena Image Library | Visualization and analysis of 3D biopolymer structures | http://www.imb-jena.de/IMAGE.html | |
| IMGT/3Dstructure-DB | Sequences and 3D structures of vertebrate immunoglobulins, T cell receptors and MHC proteins | http://imgt3d.igh.cnrs.fr/ | |
| ISSD | Integrated sequence–structure database | http://www.protein.bio.msu.su/issd | |
| LPFC | Library of protein family core structures | http://www-smi.stanford.edu/projects/helix/LPFC | |
| MMDB | NCBI's database of 3D structures, part of NCBI Entrez | http://www.ncbi.nlm.nih.gov/Structure | |
| E-MSD | EBI's macromolecular structure database | http://www.ebi.ac.uk/msd | |
| ModBase | Annotated comparative protein structure models | http://alto.compbio.ucsf.edu/modbase-cgi/index.cgi | |
| MolMovDB | Database of macromolecular movements: descriptions of protein and macromolecular motions, including movies | http://bioinfo.mbb.yale.edu/MolMovDB/ | |
| PALI | Phylogeny and alignment of homologous protein structures | http://pauling.mbu.iisc.ernet.in/~pali | |
| PASS2 | Structural motifs of protein superfamilies | http://ncbs.res.in/~faculty/mini/campass/pass.html | |
| PepConfDB | A database of peptide conformations | http://www.peptidome.org/products/list.htm | |
| PDB | Protein structure databank: all publicly available 3D structures of proteins and nucleic acids | http://www.rcsb.org/pdb | |
| PDB-REPRDB | Representative protein chains, based on PDB entries | http://mbs.cbrc.jp/pdbreprdb-cgi/reprdb_menu.pl | |
| PDBsum | Summaries and analyses of PDB structures | http://www.biochem.ucl.ac.uk/bsm/pdbsum | |
| PDB_TM | Transmembrane proteins with known 3D structure | http://www.enzim.hu/PDB_TM/ | |
| Protein Folding Database | Experimental data on protein folding | http://pfd.med.monash.edu.au | |
| SCOP | Structural classification of proteins | http://scop.mrc-lmb.cam.ac.uk/scop | |
| Sloop | Classification of protein loops | http://www-cryst.bioc.cam.ac.uk/~sloop/ | |
| Structure Superposition Database | Pairwise superposition of TIM-barrel structures | http://ssd.rbvi.ucsf.edu/ | |
| SWISS-MODEL Repository | Database of annotated 3D protein structure models | http://swissmodel.expasy.org/repository | |
| SUPERFAMILY | Assignments of proteins to structural superfamilies | http://supfam.org/ | |
| SURFACE | Surface residues and functions annotated, compared and evaluated: a database of protein surface patches | http://cbm.bio.uniroma2.it/surface | |
| TargetDB | Target data from worldwide structural genomics projects | http://targetdb.pdb.org/ | |
| 3D-GENOMICS | Structural annotations for complete proteomes | http://www.sbg.bio.ic.ac.uk/3dgenomics | |
| 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 | |||
| Genew | Human gene nomenclature: approved gene symbols | http://www.gene.ucl.ac.uk/nomenclature | |
| GO | Gene ontology consortium database | http://www.geneontology.org/ | |
| GOA | EBI's gene ontology annotation project | http://www.ebi.ac.uk/GOA | |
| IUBMB Nomenclature database | Nomenclature of enzymes, membrane transporters, electron transport proteins and other proteins | http://www.chem.qmul.ac.uk/iubmb | |
| IUPAC Nomenclature database | Nomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commission | http://www.chem.qmul.ac.uk/iupac | |
| IUPHAR-RD | The International Union of Pharmacology recommendations on receptor nomenclature and drug classification | http://www.iuphar-db.org/iuphar-rd/ | |
| PANTHER | Gene products organized by biological function | http://panther.celera.com/ | |
| UMLS | Unified medical language system | http://umlsks.nlm.nih.gov/ | |
| 5.1.1. Taxonomy and Identification | |||
| ICB | gyrB database for identification and classification of bacteria | http://seasquirt.mbio.co.jp/icb/index.php | |
| NCBI Taxonomy | Names of all organisms represented in GenBank | http://www.ncbi.nlm.nih.gov/Taxonomy/ | |
| PANDIT | Protein and associated nucleotide domains with inferred trees | http://www.ebi.ac.uk/goldman-srv/pandit/ | |
| RIDOM | rRNA-based differentiation of medical microorganisms | http://www.ridom-rdna.de/ | |
| RDP-II | Ribosomal database project | http://rdp.cme.msu.edu | |
| Tree of Life | Information on phylogeny and biodiversity | http://phylogeny.arizona.edu/tree/phylogeny.html | |
| 5.2. General genomics databases | |||
| COG | Clusters of orthologous groups of proteins | http://www.ncbi.nlm.nih.gov/COG | |
| COGENT | Complete genome tracking: predicted peptides from fully sequenced genomes | http://maine.ebi.ac.uk:8000/services/cogent/ | |
| CORG | Comparative regulatory genomics: conserved non-coding sequence blocks | http://corg.molgen.mpg.de/ | |
| DEG | Database of essential genes from bacteria and yeast | http://tubic.tju.edu.cn/deg | |
| 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 | |
| EGO | Eukaryotic gene orthologs: orthologous DNA sequences in the TIGR gene indices | http://www.tigr.org/tdb/tgi/ego/ | |
| EMGlib | Enhanced microbial genomes library: completely sequenced genomes of unicellular organisms | http://pbil.univ-lyon1.fr/emglib/emglib.html | |
| 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 | |
| ERGOLight | Integrated biochemical data on nine bacterial genomes: publicly available portion of the ERGO database | http://www.ergo-light.com/ERGO | |
| FusionDB | Database of bacterial and archaeal gene fusion events | http://igs-server.cnrs-mrs.fr/FusionDB | |
| Genome Atlas | DNA structural properties of sequenced genomes | http://www.cbs.dtu.dk/services/GenomeAtlas/ | |
| 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 | |
| Genome Reviews | Integrated view of complete genomes | http://www.ebi.ac.uk/GenomeReviews/ | |
| GOLD | Genomes online database: a listing of completed and ongoing genome projects | http://www.genomesonline.org/ | |
| HGT-DB | Putative horizontally transferred genes in prokaryotic genomes | http://www.fut.es/~debb/HGT/ | |
| Integr8 | Functional classification of proteins in whole genomes | http://www.ebi.ac.uk/integr8/ | |
| KEGG | Kyoto encyclopedia of genes and genomes: integrated suite of databases on genes, proteins and metabolic pathways | http://www.genome.jp/kegg | |
| MBGD | Microbial genome database for comparative analysis | http://mbgd.genome.ad.jp/ | |
| ORFanage | Database of orphan ORFs (ORFs with no homologs) in complete microbial genomes | http://www.cs.bgu.ac.il/~nomsiew/ORFans | |
| PACRAT | Archaeal and bacterial intergenic sequence features | http://www.biosci.ohio-tate.edu/~pacrat | |
| PartiGeneDB | Assembled partial genomes for 250 eukaryotic organisms | http://www.partigenedb.org/ | |
| PEDANT | Results of an automated analysis of genomic sequences | http://pedant.gsf.de/ | |
| TIGR Microbial Database | Lists of completed and ongoing genome projects with links to complete genome sequences | http://www.tigr.org/tdb/mdb/mdbcomplete.html | |
| TIGR Comprehensive Microbial Resource | Various data on complete microbial genomes: uniform annotation, properties of DNA and predicted proteins | http://www.tigr.org/CMR | |
| TransportDB | Predicted membrane transporters in complete genomes, classified according to the TC classification system | http://www.membranetransport.org/ | |
| 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 | |||
| HCVDB | The hepatitis C virus database | http://hepatitis.ibcp.fr/ | |
| HIV Drug Resistance Database | HIV mutations that confer resistance to anti-HIV drugs | http://resdb.lanl.gov/Resist_DB/default.htm | |
| HIV Molecular Immunology Database | HIV epitopes | http://hiv-web.lanl.gov/immunology/ | |
| HIV RT and Protease Sequence Database | HIV reverse transcriptase and protease sequences | http://hivdb.stanford.edu/ | |
| NCBI Viral Genomes | Viral genome resource at NCBI | http://www.ncbi.nlm.nih.gov/genomes/VIRUSES/viruses.html | |
| Poxvirus.org | Poxvirus genomic sequences and gene annotation | http://www.poxvirus.org/ | |
| T4-like genome database | Sequences of T4-like bacteriophages from various sources | http://phage.bioc.tulane.edu/ | |
| VIDA | Homologous viral protein families database | http://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA.html | |
| VIPER | Virus particle explorer: virus capsid structures | http://mmtsb.scripps.edu/viper | |
| VirOligo | Virus-specific oligonucleotides for PCR and hybridization | http://viroligo.okstate.edu/ | |
| 5.3.2. Prokaryotes | |||
| BacMap | Picture atlas of annotated bacterial genomes | http://wishart.biology.ualberta.ca/BacMap | |
| MetaGrowth | Growth requirements of bacterial pathogens | http://igs-server.cnrs-mrs.fr/axenic/ | |
| PGTdb | Prokaryotic growth temperature database | http://pgtdb.csie.ncu.edu.tw/ | |
| 5.3.2.1. Escherichia coli | |||
| ASAP | A systematic annotation package for community analysis of E.coli and related genomes | https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm | |
| 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 | |
| coliBase | A database for E.coli, Salmonella and Shigella | http://colibase.bham.ac.uk/ | |
| Colibri | E.coli genome database at Institut Pasteur | http://genolist.pasteur.fr/Colibri/ | |
| EchoBASE | Post-genomic studies of Escherichia coli | http://www.ecoli-york.org/ | |
| Essential genes in E.coli | First results of an E.coli gene deletion project | http://www.genome.wisc.edu/resources/essential.htm | |
| GenoBase | E.coli genome database at Nara Institute | http://ecoli.aist-nara.ac.jp/ | |
| GenProtEC | E.coli K12 genome and proteome database | http://genprotec.mbl.edu | |
| PEC | Profiling of E.coli chromosome | http://shigen.lab.nig.ac.jp/ecoli/pec | |
| EcoCyc | E.coli K12 genes, metabolic pathways, transporters and gene regulation | http://ecocyc.org/ | |
| EcoGene | Sequence and literature data on E.coli genes and proteins | http://bmb.med.miami.edu/EcoGene/EcoWeb/ | |
| RegulonDB | Transcriptional regulation and operon organization in E.coli | http://www.cifn.unam.mx/Computational_Genomics/regulondb/ | |
| 5.3.2.2. Bacillus subtilis | |||
| BSORF | Bacillus subtilis genome database at Kyoto U. | http://bacillus.genome.ad.jp/ | |
| NRSub | Non-redundant Bacillus subtilis database at U. Lyon | http://pbil.univ-lyon1.fr/nrsub/nrsub.html | |
| SubtiList | Bacillus subtilis genome database at Institut Pasteur | http://genolist.pasteur.fr/SubtiList/ | |
| 5.3.2.3. Other bacteria | |||
| BioCyc | Pathway/genome databases for many bacteria | http://biocyc.org/ | |
| CampyDB | Database for Campylobacter genome analysis | http://campy.bham.ac.uk/ | |
| ClostriDB | Finished and unfinished genomes of Clostridium spp. | http://clostri.bham.ac.uk/ | |
| CIDB | Chlamydia Interactive Database: gene expression data | http://www.it.deakin.edu.au/CIDB | |
| CyanoBase | Cyanobacterial genomes | http://www.kazusa.or.jp/cyano | |
| LeptoList | Leptospira interrogans genome | http://bioinfo.hku.hk/LeptoList | |
| MolliGen | Genomic data on mollicutes | http://cbi.labri.fr/outils/molligen/ | |
| PseudoCAP | Pseudomonas aeruginosa genome database and community annotation project | http://www.pseudomonas.com/ | |
| RsGDB | Rhodobacter sphaeroides genome | http://www.hgsc.bcm.tmc.edu/projects/microbial/Rsphaeroides/ | |
| VirFact | Bacterial virulence factors and pathogenicity islands | http://virfact.burnham.org/ | |
| Virulence Factors | Reference database for microbial virulence factors | http://zdsys.chgb.org.cn/VFs/main.htm | |
| 5.3.3. Unicellular eukaryotes | |||
| ApiEST-DB | EST sequences from various Apicomplexan parasites | http://www.cbil.upenn.edu/paradbs-servlet | |
| CryptoDB | Cryptosporidium parvum genome database | http://cryptodb.org/ | |
| Diatom EST Database | ESTs from two diatom algae, Thalassiosira pseudonana and Phaeodactylum tricornutum | http://avesthagen.sznbowler.com/ | |
| DictyBase | Universal resource for Dictyostelium discoideum | http://dictybase.org/ | |
| Full-Malaria | Full-length cDNA library from erythrocytic-stage Plasmodium falciparum | http://fullmal.ims.u-tokyo.ac.jp/ | |
| GeneDB | Curated database for various Sanger-sequenced genomes | http://www.genedb.org/ | |
| LumbriBASE | ESTs of the earthworm Lumbricus rubellus | http://www.earthworms.org/ | |
| PlasmoDB | Plasmodium genome database | http://plasmodb.org/ | |
| TcruziDB | Trypanosoma cruzi genome database | http://tcruzidb.org/ | |
| ToxoDB | Toxoplasma gondii genome database | http://toxodb.org/ | |
| 5.3.4. Fungi | |||
| 5.3.4.1. Yeasts | |||
| AGD | Ashbya gossypii genome database | http://agd.unibas.ch | |
| CandidaDB | Candida albicans genome database | http://genolist.pasteur.fr/CandidaDB | |
| Candida Genome | Candida albicans genome database | http://www.candidagenome.org/ | |
| CYGD | MIPS Comprehensive yeast genome database | http://mips.gsf.de/proj/yeast | |
| Génolevures | A comparison of S.cerevisiae and 14 other yeast species | http://cbi.labri.fr/Genolevures | |
| PROPHECY | Profiling of phenotypic characteristics in yeast | http://prophecy.lundberg.gu.se/ | |
| SCMD | Saccharomyces cerevisiae morphological database: micrographs of budding yeast mutants | http://yeast.gi.k.u-tokyo.ac.jp/ | |
| SCPD | Saccharomyces cerevisiae promoter database | http://cgsigma.cshl.org/jian | |
| SGD | Saccharomyces genome database | http://www.yeastgenome.org/ | |
| TRIPLES | Transposon-insertion phenotypes, localization and expression in Saccharomyces | http://ygac.med.yale.edu/triples/ | |
| YDPM | Yeast deletion project and mitochondria database | http://www-deletion.stanford.edu/YDPM/YDPM_index.html | |
| Yeast Intron Database | Ares lab database of splicesomal introns in S.cerevisiae | http://www.cse.ucsc.edu/research/compbio/yeast_introns.html | |
| Yeast snoRNA Database | Yeast small nucleolar RNAs | http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html | |
| yMGV | Yeast microarray global viewer | http://www.transcriptome.ens.fr/ymgv/ | |
| YRC PDR | Yeast resource center public data repository | http://www.yeastrc.org/pdr/ | |
| 5.3.4.2. Other fungi | |||
| CADRE | Central Aspergillus data repository | http://www.cadre.man.ac.uk/ | |
| COGEME | Phytopathogenic fungi and oomycete EST database | http://cogeme.ex.ac.uk | |
| MNCDB | MIPS Neurospora crassa database | http://mips.gsf.de/proj/neurospora/ | |
| OGD | Oomycete Genomics Database: ESTs and annotation | http://www.oomycete.net/ | |
| 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 | |||
| C.elegans Project | Genome sequencing data at the Sanger Institute | http://www.sanger.ac.uk/Projects/C_elegans | |
| Intronerator | Introns and splicing in C.elegans and C.briggsae | http://www.cse.ucsc.edu/~kent/intronerator/ | |
| RNAiDB | RNAi phenotypic analysis of C.elegans genes | http://www.rnai.org/ | |
| WILMA | C.elegans annotation database | http://www.came.sbg.ac.at/wilma/ | |
| WorfDB | C.elegans ORFeome | http://worfdb.dfci.harvard.edu/ | |
| 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 | |||
| FlyBase | Drosophila sequences and genomic information | http://flybase.bio.indiana.edu/ | |
| FlyBrain | Database of the Drosophila nervous system | http://flybrain.neurobio.arizona.edu | |
| FlyMine | Integration of insect genomic and proteomic data | http://www.flymine.org/ | |
| FlyTrap | Drosophila mutants created using GFP protein trap strategy | http://flytrap.med.yale.edu/ | |
| GadFly | Genome annotation database of Drosophila | http://www.fruitfly.org | |
| GeniSys | Enhancer- and promoter-inserted mutants of Drosophila | http://genisys.kaist.ac.kr:8080/ | |
| DPDB | Drosophila polymorphism database | http://dpdb.uab.es/ | |
| Drosophila microarray project | Data and tools for Drosophila gene expression studies | http://www.flyarrays.com/fruitfly | |
| InterActive Fly | Drosophila genes and thei | ||