Black

1.1. International Nucleotide Sequence Database Collaboration
1.2. DNA sequences: genes, motifs and regulatory sites

1.2.1. Coding and coding DNA
1.2.2. Gene structure, introns and exons, splice sites
1.2.3. Transcriptional regulator sites and transcription factors

3.1. General sequence databases
3.2. Protein properties
3.3. Protein localization and targeting
3.4. Protein sequence motifs and active sites
3.5. Protein domain databases; protein classification
3.6. Databases of individual protein families

4.1. Small molecules
4.2. Carbohydrates
4.3. Nucleic acid structure
4.4. Protein structure

5.1. Genome annotation terms, ontologies and nomenclature

5.1.1. Taxonomy and Identification

5.2. General genomics databases
5.3. Organism-specific databases

5.3.1. Viruses
5.3.2. Prokaryotes

5.3.2.1. Escherichia coli
5.3.2.2. Bacillus subtilis
5.3.2.3. Other bacteria

5.3.3. Unicellular eukaryotes
5.3.4. Fungi

5.3.4.1. Yeasts
5.3.4.2. Other fungi

5.3.5. Invertebrates

5.3.5.1. Caenorhabditis elegans
5.3.5.2. Drosophila melanogaster
5.3.5.3. Other invertebrates

6.1. Enzymes and Enzyme Nomenclature
6.2. Metabolic Pathways
6.3. Intermolecular Interactions and Signaling Pathways

7.1. Model organisms, comparative genomics
7.2. Human genome databases, maps and viewer
7.3. Human proteins

8.1. General Databases
8.2. Human Mutations Databases

8.2.1. General polymorphism databases
8.2.2. Cancer
8.2.3. Gene-, system- or disease-specific

11.1. Drugs and drug design
11.2. Probes
11.3. Unclassified databases

12.1. Mitochondrial Genes and Proteins

13.1. General plant databases
13.2. Arabidopsis thaliana
13.3. Rice
13.4. Other plants

ÏêϸÁбí

Table 1. Molecular Biology Database Collection^a

No.b Database name Full name and/or description URL 1. Nucleotide Sequence Databases 1.1. International Nucleotide Sequence Database Collaboration 1 DDBJ¡ªDNA 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¨Cintron 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¨Cnucleic 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¡ªKinases in Genomes S/T/Y-specific protein kinases encoded in complete genomes http://hodgkin.mbu.iisc.ernet.in/~king 519 Knottins Database of knottins¡ªsmall 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¡ªUppsala http://xray.bmc.uu.se/hicup 402 AANT Amino acid¨Cnucleotide 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¨Cstructure 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¨Cstructure 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 anddrug 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 G¨¦nolevures 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 http://www.ncgr.org/pathdb 117 UM-BBD University of Minnesota biocatalysis and biodegradation database http://umbbd.ahc.umn.edu/ 6.3. Intermolecular Interactions and Signaling Pathways 633 3DID 3D interacting domains: domain¨Cdomain interactions in proteins with known 3D structures http://3did.embl.de 405 aMAZE A system for the annotation, management, and analysis of biochemical and signalling pathway networks http://www.amaze.ulb.ac.be/ 103 BIND Biomolecular interaction network database http://www.bind.ca 419 BioCarta Online maps of metabolic and signaling pathways http://www.biocarta.com/genes/allPathways.asp 422 BRITE Biomolecular relations in information transmission and expression, part of KEGG http://www.genome.ad.jp/brite 659 DDIB Database of domain interactions and binding http://www.ddib.org/ 104 DIP Database of interacting proteins: experimentally determined protein¨Cprotein interactions http://dip.doe-mbi.ucla.edu 105 DRC Database of ribosomal crosslinks http://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc 329 GeneNet Database on gene network components http://wwwmgs.bionet.nsc.ru/mgs/gnw/genenet 664 hp-DPI Database of protein interactions in Helicobacter pylori http://dpi.nhri.org.tw/hp/ 688 HPID Human protein interaction database http://www.hpid.org/ 507 IntAct project Protein¨Cprotein interaction data http://www.ebi.ac.uk/intact 770 Inter-Chain Beta-Sheets Protein¨Cprotein interactions mediated by interchain beta-sheet formation http://www.igb.uci.edu/servers/icbs/ 510 InterDom Putative protein domain interactions http://interdom.lit.org.sg 718 PDZBase Protein¨Cprotein interactions involving PDZ domains http://icb.med.cornell.edu/services/pdz/start 749 Protein-protein interfaces Interacting residues in protein¨Cprotein interfaces in PDB http://home.ku.edu.tr/~okeskin/INTERFACE/INTERFACES.html 773 PINdb Proteins interacting in nucleus (human and yeast) http://pin.mskcc.org/ 748 POINT Prediction of human protein¨Cprotein interactome http://point.nchc.org.tw/ 616 PSIbase Interaction of proteins with known 3D structures http://psimap.kaist.ac.kr/ 612 Reactome A knowledgebase of biological pathways http://www.reactome.org/ 571 ROSPath Reactive oxygen species (ROS) signaling pathway http://rospath.ewha.ac.kr/ 395 STCDB Signal transductions classification database http://bibiserv.techfak.uni-bielefeld.de/stcdb/ 582 STRING Predicted functional associations between proteins http://string.embl.de/ 341 TRANSPATH Gene regulatory networks and microarray analysis http://www.biobase.de/pages/products/databases.html 7. Human and other Vertebrate Genomes 7.1. Model organisms, comparative genomics 63 ACeDB C.elegans, S.pombe and human genomic information http://www.acedb.org/ 26 AllGenes Human and mouse gene, transcript and protein annotation http://www.allgenes.org/ 65 ArkDB Genome databases for farm and other animals http://www.thearkdb.org/ 647 ChickVD Sequence variation in the chicken genome http://chicken.genomics.org.cn/ 286 Cre Transgenic Database Cre transgenic mouse lines with links to publications http://www.mshri.on.ca/nagy/ 660 DED Database of evolutionary distances http://warta.bio.psu.edu/DED/ 27 Ensembl Annotated information on eukaryotic genomes http://www.ensembl.org/ 465 FANTOM Functional annotation of mouse full-length cDNA clones http://fantom2.gsc.riken.go.jp 468 FREP Functional repeats in mouse cDNAs http://facts.gsc.riken.go.jp/FREP/ 673 GALA Genomic alignment, annotation and experimental results http://gala.cse.psu.edu/ 347 GenetPig Genes controlling economic traits in pig http://www.infobiogen.fr/services/Genetpig 605 HomoloGene Automatically detected homologous genes in complete eukaryotic genomes http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=homologene 690 Inparanoid A database of eukaryotic orthologs http://inparanoid.cgb.ki.se/ 696 IPI International protein index: non-redundant sets of human, mouse and rat proteins http://www.ebi.ac.uk/IPI 777 KaryotypeDB Karyotype and chromosome information for animal and plant species http://www.nenno.it/karyotypedb/ 400 KOG Eukaryotic orthologous groups of proteins http://www.ncbi.nlm.nih.gov/COG/new/shokog.cgi 87 Mouse Genome Informatics Formerly mouse genome database http://www.informatics.jax.org/ 540 MTID Mouse transposon insertion database http://mouse.ccgb.umn.edu/transposon/ 703 NegProt Negative Proteome: a tool for comparison of complete proteomes http://superfly.ucsd.edu/negprot 556 PEDE Pig EST data explorer: full-length cDNAs and ESTs http://pede.gene.staff.or.jp/ 665 PhenomicDB Comparison of phenotypes of orthologous genes in human and model organisms http://www.phenomicdb.de/ 724 Polymorphix A database of sequence polymorphisms http://pbil.univ-lyon1.fr/polymorphix/query.php 93 Rat Genome Database Rat genetic and genomic data http://rgd.mcw.edu/ 625 RatMap Rat genome tools and data http://ratmap.org/ 751 TAED The adaptive evolution database: a phylogeny-based tool for comparative genomics http://www.bioinfo.no/tools/TAED 5 TIGR Gene Indices Organism-specific databases of EST and gene sequences http://www.tigr.org/tdb/tgi.shtml 6 UniGene Unified clusters of ESTs and full-length mRNA sequences http://www.ncbi.nlm.nih.gov/UniGene/ 319 UniSTS Unified view of sequence tagged sites with mapping data http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unists 783 VEGA Vertebrate genome annotation: a repository for manual annotation of finished vertebrate genome sequences http://vega.sanger.ac.uk/ 101 ZFIN Zebrafish information network http://zfin.org/ 7.2. Human genome databases, maps and viewers 27 Ensembl Annotated information on eukaryotic genomes http://www.ensembl.org/ 404 AluGene Complete Alu map in the human genome http://alugene.tau.ac.il/ 349 CroW 21 Human chromosome 21 database http://bioinfo.weizmann.ac.il/crow21/ 55 GB4-RH Genebridge4 human radiation hybrid maps http://www.sanger.ac.uk/Software/RHserver/RHserver.shtml 56 GDB Human genes and genomic maps http://www.gdb.org/ 57 GenAtlas Human genes, markers and phenotypes http://www.genatlas.org/ 350 GeneCards Integrated database of human genes, maps, proteins and diseases http://bioinfo.weizmann.ac.il/cards/ 348 GeneLoc Gene location database (formerly UDB¡ªUnified database for human genome mapping) http://genecards.weizmann.ac.il/geneloc/ 327 GeneNest Gene indices of human, mouse, zebrafish, etc. http://genenest.molgen.mpg.de/ 59 GenMapDB Mapped human BAC clones http://genomics.med.upenn.edu/genmapdb 35 Gene Resource Locator Alignment of ESTs with finished human sequence http://grl.gi.k.u-tokyo.ac.jp/ 324 HOWDY Human organized whole genome database http://www-alis.tokyo.jst.go.jp/HOWDY/ 60 HuGeMap Human genome genetic and physical map data http://www.infobiogen.fr/services/Hugemap

^a Each database is shown in the list only once, often in a category that was arbitrarily chosen among two or three appropriate ones. In the online version of this list at the NAR website (http://nar.oupjournals.org/), a database can be listed under two categories.

^b Accession number of the database in the online list; can be used to view the database summary, e.g. http://www3.oup.co.uk/nar/database/summary/1 shows the summary for DDBJ.