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Nucleic Acids Res by wulinqing

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									Supplementary Table 1. NAR Molecular Biology Database Collection: 2008 updatea

Nob    Database namec         Full name and/or description                                     URL
       1. Nucleotide Sequence Databases
       1.1. International Nucleotide Sequence Database Collaboration
 1     DDBJ - DNA Data Bank   All known nucleotide and protein sequences             
       of Japan
 2     EMBL Nucleotide        All known nucleotide and protein sequences             
       Sequence Database
 3     GenBank                All known nucleotide and protein sequences             
       1.2. Coding and coding DNA: genes, motifs and regulatory sites
403    ACLAME                 A classification of genetic mobile elements            
337    CORG                   Comparative Regulatory Genomics: conserved non-coding blocks
                              in vertebrate species
 30    CUTG                   Codon Usage Tabulated from GenBank                     
1157   ECRbase                Database of Evolutionary Conserved Regions, promoters, and
                              transcription factor binding sites
668    Entrez Gene            Gene-centered information at NCBI                      
669    FESD                   Functional Element SNPs Database: SNPs located within  
                              promoters, UTRs, etc., of human genes
468    FREP                   Functional Repeats in mouse cDNAs                      
480    Genetic Codes          Genetic codes in various organisms and organelles      
1079   GISSD                  Group I Intron Sequence and Structure Database         
1083   GyDB                   Gypsy database of mobile genetic elements              
 825   HumHot                 Human meiotic recombination hot spots                  
 932   InSatDb                Sequences and properties of insect microsatellites     
 832   ISfinder               Insertion sequences from bacteria and archaea          
 512   Islander               Pathogenicity islands and prophages in bacterial genomes
 697   L1Base                 Functional annotation and prediction of LINE-1 elements
  19   MethDB                 DNA methylation data, patterns and profiles            
 343   MICdb                  Prokaryotic microsatellites                            
 707   NPRD                   Nucleosome Positioning Region Database                 
931    OriDB                  DNA Replication Origin Database: Confirmed and predicted sites
 551   PACRAT                 Archaeal and bacterial intergenic sequence features              No longer maintained
 608   PANDIT                 Protein and associated nucleotide domains with inferred trees
 933   Patome                 Annotated sequences from patents and patent applications
 958   PolymiRTS              Polymorphism in microRNA Target Site                   
1007         Pseudogenes in eukaryotic and prokaryotic genomes      
  21   RECODE                 Genes using programmed translational recoding in their 
391    RefSeq                 Reference Sequence database: an integrated, non-redundant set
                              of genomic DNA, RNA, and protein sequences
1019   RetrOryza              LTR-retrotransposons in rice                           
 309   S/MARt DB              Nuclear scaffold/matrix attached regions               
1013   SNPSTR                 Microsatellite compound markers in 5 vertebrate genomes
  47   STRBase                Short tandem DNA repeats database                      
 929   Synthetic Gene DB      Synthetic genes described in peer-reviewed literature  
 588   TIGR plant repeat DB   Classification of repetitive sequences in plant genomes
1141   TranspoGene            Transposed elements influence on the transcriptome of seven
                              vertebrates and invertebrates
1035   TRDB                   Tandem repeats in genomic DNA                          
1143   UgMicroSatdb           UniGene MicroSatellite database: short tandem repeats from
                              various eukaryotic genomes
320    UniVec                 Vector sequences, adapters, linkers and primers used in DNA
                              cloning, used to check for vector contamination
 252   UTRdb/UTRsite          5'- and 3'-UTRs of eukaryotic mRNAs                    
1146   UTRome                 3'UTRs and their functional elements in C. elegans     
 302   Vectordb               Characterization and classification of nucleic acid vectors
 968   VISTA Enhancer         Enhancer elements in the human genome                  
       1.3. Gene structure, introns and exons, splice sites
414    ASAP II                Comparative analysis of alternative splicing in animal species
 10    ASDB                   Alternative Splicing Database: protein products and expression
                              patterns of alternatively-spliced genes
639    ASHESdb                Alternatively Spliced Human genes by Exon Skipping     
 28    ASTD                   Alternative Splicing and Transcript Diversity database 
920    ATD                    Alternate transcript diversity database                          Superseded by ASTD, no. 28
803    ChimerDB               Chimeric (fusion) sequences in human, rat and mouse    
450    EASED                  Extended Alternatively Spliced EST Database            
667    ECgene                 Genome annotation for alternative splicing             
631    EDAS                   EST-derived alternative splicing database              
 32    EID                     Exon-intron database                                       
 34    ExInt                   Exon–intron structure of eukaryotic genes                  
913    ExtraTRAIN              Extragenic regions and transcriptional regulators in bacteria and
782    FUGOID                  Functional genomics of organelle introns database          
 970   H-DBAS                  Human database of alternative splicing                     
 821   Hollywood               Exon annotation database                                   
  36   HS D                    Homo Sapiens Splice Sites Dataset                          
 238   Intronerator            Alternative splicing in C. elegans and C. briggsae         
1122   ProSAS                  Protein Structure and Alternative Splicing: effects of alternative
                               splicing events on protein structure
46     SpliceDB                Canonical and non-canonical mammalian splice sites         
746    SpliceInfo              Modes of alternative splicing in human genome              
580    SpliceNest              Visualizing Splicing of Genes from EST Data                
927    TassDB                  TAndem Splice Site Database                                
937    U12DB                   Database of orthologous U12-type spliceosomal introns      
305    Xpro                    Eukaryotic protein-encoding DNA sequences, both intron-    
                               containing and intron-less genes
342    Yeast Intron Database   Ares lab database of splicesomal introns in S. cerevisiae  
       1.4. Transcriptional regulator sites and transcription factors
 795   ABS                     Annotated regulatory binding sites from orthologous promoters
 231   ACTIVITY                Functional DNA/RNA site activity                           
 308   ASPD                    Artificial selected proteins/peptides database             
 805   CisRed                  Human regulatory DNA sequence motifs                       
1058   CMGSDB                  Computational models for gene silencing in C. elegans      
1062   COXPRESdb               Coexpressed genes and networks in human and mouse          
1063   CTCF Binding Site DB    Experimentally identified and predicted CTCF binding sties 
 807   DBD                     Transcription factor prediction database                   
  31   DBTBS                   Bacillus subtilis promoters and transcription factors      
 591   DBTSS                   Database of transcriptional start sites                    
 663   DoOP                    Databases of Orthologous Promoters: chordates and plants   
 106   DPInteract              Binding sites for E. coli DNA-binding proteins             
  33   EPD                     Eukaryotic promoter database                               
 329   GeneNet                 Database on gene network components                        
1036   GenomeTraFaC            Conserved regulatory elements of human and mouse genes     
 823   HTPSELEX                Transcription factor binding site sequences obtained using high-
                           throughput SELEX method
 516   JASPAR              PSSMs for transcription factor DNA-binding sites               
 700   MAPPER              Putative transcription factor binding sites in various genomes 
 842   MPromDB             Mammalian promoter database                                    
 846   ODB                 Operon database                                                
 185   ooTFD               Object-oriented transcription factors database                 
1107   ORegAnno            Open REGulatory ANNOtation database                            
 711   Osteo-Promoter DB   Genes in osteogenic proliferation and differentiation          
  40   PLACE               Plant cis-acting regulatory DNA elements                       
  41   PlantCARE           Plant promoters and cis-acting regulatory elements             
563    PlantProm           Plant promoter sequences for RNA polymerase II                 
1117   PlantTFDB           Plant Transcription Factor Database                            
1005   PReMod              Predicted transcriptional regulatory modules in the human genome
 566   PRODORIC            Prokaryotic database of gene regulation networks               
  42   PromEC              E. coli promoters with experimentally-identified transcriptional start
1123   ProTISA             Translation Initiation Site Annotation in prokaryotic genomes  
 116   RegulonDB           Transcriptional regulation and operon organization in E.coli   
  45   rSNP Guide          SNPs in regulatory gene regions                                
 577   SCPD                Saccharomyces cerevisiae promoter database                     
 246   SELEXdb             Selected DNA/RNA functional site sequences                     
1015   SwissRegulon        Genome-wide annotations of regulatory sites in the intergenic  
       database            regions
227    TESS                Transcription element search system                            
904    TiProD              Tissue-specific promoter database                              
756    Tractor_DB          Transcription factors in gamma-proteobacteria database         
345    TRANSCompel         Transcriptional regulation, composite regulatory elements      
 340   TRANSFAC            Transcription factors, gene regulation, positional weight matrices
1141   TransfactomeDB      Nucleotide sequence specificity and condition-specific regulatory
                           activity of trans-acting factors
341    TRANSPATH           Signal transduction pathways, vizualization and expression data
 48    Transterm           Codon usage, start and stop signals                            
757    TRED                Transcriptional regulatory element database                    
 49    TRRD                Transcription regulatory regions of eukaryotic genes           
314    TrSDB               Transcription factor database                                  
792    YEASTRACT           Yeast transcriptional regulation                               
       2. RNA Sequence, Structure and Functions
229    16S and 23S rRNA          16S and 23S ribosomal RNA mutations                       
       Mutation Database
1041   3D rRNA modification      Locations of modified rRNA nucleotides within the 3D structure of
       maps                      the ribosome                                                        ap/
 230   5S rRNA Database          5S rRNA sequences                                         
 411   Aptamer Database          Small RNA/DNA molecules binding nucleic acids, proteins   
 232   ARED                       AU-rich element-containing mRNAs                         
 797   Argonaute                 Gene regulation by mammalian microRNAs                    
 984   dbRES                     Database of known RNA editing sites                       
 463   European rRNA DB          All complete or nearly complete rRNA sequences            
1027   fRNAdb                    Functional RNA Database: noncoding transcripts that affect gene
878    Greengenes                Multiple sequence alignment of prokaryotic 16S rDNA       
820    GRSDB                     G-rich sequences database                                 
490    G-tRNA-db                 Genomic tRNA Database                                     
236    Guide RNA Database                                                                            No longer maintained
 76    HIV Sequence DB           HIV RNA sequences                                         
689    HuSiDa                    Human siRNA database                                      
 237   HyPaLib                   Hybrid pattern library: structural elements in classes of RNA       Not actively maintained
 379   IRESdb -                  the Internal Ribosome Entry Site database                 
 831   IRESite                   Experimentally studied internal ribosome entry sites      
 838   MeRNA                     Metal ion binding sites in RNA                            
1097              microRNA target predictions and expression profiles       
 529   miRBase                   MicroRNA sequences, names, and predicted targets in animals
1098   miRGator                  microRNA target prediction, functional analysis, and gene 
                                 expression data
994    miRGen                    Animal microRNAs located in introns, exons, UTRs, pseudogenes
                                 and CpG islands
895    miRNAMap                  microRNA precursors and their mapping to targets in vertebrate
378    Mobile group II introns   Database for mobile group II introns                      
840    MODOMICS                  Database of RNA modification pathways                     
997    NATsDB                    Natural Antisense Transcripts database                    
380    NCIR                      Non-Canonical Interactions in RNA                         
381    ncRNAs database           Non-coding RNAs with regulatory functions                 
705    NONCODE                   Database of noncoding RNAs                                
845    NPInter                   Noncoding RNA-protein interactions                        
1114   piRNABank               Sequences and properties of Piwi-interacting RNAs (piRNAs) in
                               human, mouse and rat
 564   Plant snoRNA DB         snoRNA genes in plant species                         
 240   PLANTncRNAs                                                                             No longer maintained
 241   PLMItRNA                Mitochondrial tRNA genes in photosynthetic eukaryotes 
 723   PolyA_DB                Database of mammalian mRNA polyadenylation            
 242   PseudoBase              Database of RNA pseudoknots                           
1009   REDIdb                  An RNA editing database                               
 382   Rfam                    Non-coding RNA families                               
 243   RDP-II                  Ribosomal Database Project                            
 244   RISSC                   Ribosomal Internal Spacer Sequence Collection         
 245   RNA Modification DB     Naturally modified nucleosides in RNA                 
 900   RNA SSTRAND             RNA secondary structure data and structural motifs    
 630   RNAdb                   Mammalian noncoding RNA database                      
 862   RNAi codex              Clones from mouse, human and rat shRNA libraries      
1162   siRecords               Experimentally tested mammalian siRNAs                
 629   siRNAdb                 Functional human siRNA sequences                      
 247   Small RNA Database                                                                      No longer maintained
 869   snoRNA-LBME-db          Human snoRNAs and Cajal body-specific RNAs (scaRNAs)  
 962   Sno/scaRNAbase          Small nucleolar RNAs and cajal body-specific RNAs     
 248   SRPDB                   Signal recognition particle database                  
 383   Subviral RNA DB         Database of viroids and viroid-like RNAs              
 754   The Small Subunit       Modified nucleosides in small subunit rRNA            
       rRNA Modification DB
 250   tmRDB                   tmRNA database                                        
 249   tmRNA Website           tmRNA sequences and alignments                        
 251   tRNA Sequences                                                                          Has not been updated
1148   Vir-Mir db              Prediction of viral microRNA candidate hairpins       
 254   Yeast snoRNA            Yeast small nucleolar RNAs                            
       Database                                                                                sequence/Yeast_snoRNA_Database/snoRNA_DataBa

       3. Protein Sequence Databases

       3.1. General sequence databases
163    EXProt                  Sequences of proteins with experimentally verified function
 88    MIPS resources          Munich Information Center for Protein Sequences databases
542    NCBI Protein database   All protein sequences: translated from GenBank and imported
                               from other protein databases                                    ein
714    PA-GOSUB                Protein sequences from model organisms, GO assignment and
                              subcellular localization
194    PIR                    Protein Information Resource                            
565    PRF                    Protein research foundation database of peptides        
790    TCDB                   Transporter protein classification database             
775    UniParc                UniProt archive, a repository of all protein sequences  
318    UniProt                Universal Protein knowledgebase, combined information from
                              Swiss-Prot, TrEMBL, and PIR
 197   UniProtKB\Swiss-Prot   Formerly SwissProt, part of the UniProt knowledgebase   
 198   UniProtKB\TrEMBL       Now UniProt/TrEMBL, part of the UniProt knowledgebase   
 776   UniRef                 Clustered sets of related sequences from UniProt        
1165   UniSave                UniProtKB Sequence/Annotation Version Archive           
       3.2. Protein properties
 221   AAindex                Physicochemical properties of amino acids               
 979   BindingDB              Binding affinities of protein-ligand and other complexes
 806   CyBase                 Proteins with cyclic backbones                          
 885   dbPTM                  Information on post-translational modification of proteins
 914   iProLINK               Annotated literature sources for protein features and names
1093   MALISAM                Manual alignments for structurally analogous motifs in proteins
1094   MegaMotifbase          Structural motifs in protein families and superfamilies 
 954   PIDD                   Protein inter-atomic distances database                 
 854   PINT                   Protein-protein interactions thermodynamic database     
 856   PPD                    Experimentally-determined protein pKa values            
1120   PPT-DB                 Protein Property Prediction and Testing Database        
280    ProTherm               Thermodynamic data for wild-type and mutant proteins    
1176   PRTAD                  Protein residue torsion angle database                  
 783   REFOLD                 Experimental data on protein refolding and purification 
       3.3. Protein localization and targeting
 444   DBSubLoc -             Database of protein Subcellular Localization            
 930   eSLDB                  eukaryotic proteins Subcellular Localization Database   
1021   InterFil               Human Intermediate Filament database                    
 836   LOCATE                 Subcellular localization of mouse proteins              
1022   MiCroKit               Midbody, Centrosome and Kinetochore proteins            
 226   MitoDrome              Nuclear-encoded mitochondrial proteins of Drosophila    
  85   MitoRes                Nuclear genes coding for mitochondrial proteins         
 375   NESbase                Nuclear export signals database                         
 376   NLSdb                  Nuclear localization signals                            
704    NMPdb                    Nuclear matrix associated proteins database             
706    NOPdb:                   Nucleolar proteome database                             
369    NPD                      Nuclear Protein Database                                
182    Nuclear Receptor         Nuclear receptor superfamily                            
183    NUREBASE                 Nuclear hormone receptors database                                http://www.ens-
 789   NURSA                    Nuclear receptor signaling atlas                        
 734   PSORTdb                  Protein subcellular localization in bacteria            
 745   Secreted Protein DB      Secreted proteins from human, mouse and rat             
1014   SUBA                     Subcellular localisation of Arabidopsis proteins        
 587   THGS                     Transmembrane Helices in Genome Sequences               
1140   TopDB                    Topology Data Bank of transmembrane proteins            
 589   Transmembrane             Transmembrane proteins with experimentally-characterized
       Protein Database         transmembrane topologies
       3.4. Protein sequence motifs and active sites
374    ASC                      Active Sequence Collection                              
203    Blocks                   Alignments of conserved regions in protein families     
438    COMe                     Co-Ordination of Metals etc.                            
771    CoPS                     Comprehensive peptide signature database                
440    CSA                      Catalytic Site Atlas                                    
666    eBLOCKS                  Highly conserved protein sequence blocks                
452    eF-site                  Electrostatic surface of Functional site                
206    eMOTIF                   Protein sequence motif determination and searches       
986    FireDB                   Functionally important residues in protein structures   
207    InterPro                 Integrated resource of protein families, domains and functional
179    Metalloprotein Site DB   Metal-binding sites in metalloproteins                  
209    O-GLYCBASE               O- and C-linked glycosylation sites in proteins         
717    PDBSite                  3D structure of protein functional sites                
 187   Phospho.ELM              S/T/Y protein phosphorylation sites (former PhosphoBase)
1003   Phospho3D                3D structures of protein phosphorylation sites          
 212   PRINTS                   Hierarchical gene family fingerprints                   
 193   PROMISE                  Prosthetic centers and metal ions in protein active sites
 899   ProRule                  Functional and structural information on PROSITE profiles
 215   PROSITE                  Biologically-significant protein patterns and profiles  
 732   ProTeus                  Signature sequences at the protein N- and C-termini     
 868   SitesBase                Known ligand binding sites in the PDB                   
       3.5. Protein domain databases; protein classification
622    ADDA                Database of protein domain classification                    
288    BAliBASE            Benchmark database for comparison of multiple sequence                 http://www-igbmc.u-
978    Benchmark           Protein classification benchmark collection: training/test sets for
                           machine learning
786    BIOZON              Database of gene and protein familiy classification          
204    CDD                 Conserved domain database, includes protein domains from Pfam,
                           SMART, COG and KOG databases
 205   CluSTr              Clusters of UniProt Knowledgebase and IPI proteins           
  7    COG                 Clusters of orthologous groups of proteins                   
 448   DomIns              Database of Domain Insertions                                
1068   eggNOG              Evolutionary genealogy of genes: Non-supervised Orthologous  
1069   EPGD                Eukaryotic Paralog Group Database                            
 963   EVEREST             Automatically generated protein domain families              
 671   FunShift            Functional divergence between the subfamilies of a protein   
                           domain family
470    FusionDB            Database of bacterial and archaeal gene fusion events        
200    Hits                Database of protein domains and motifs                       
266    HSSP                Homology-derived structures of proteins                      
 510   InterDom            Putative protein domain interactions                         
 208   iProClass           Integrated protein classification database                   
 844   MulPSSM             Multiple PSSMs of structural and sequence families           
1109   PairsDB             Pairwise alignments of all sequences in UniProt              
 274   PALI                Phylogeny and alignment of homologous protein structures     
 552   PANTHER             Protein sequence evolution mapped to functions and pathways  
 210   Pfam                Protein families: Multiple sequence alignments and profile hidden
                           Markov models of protein domains
 981   PhyloFacts          Phylogenomic analysis of protein families                    
 561   PIRSF               Family/superfamily classification of whole proteins          
 214   ProDom              Protein domain families                                      
 216   ProtoMap            Hierarchical classification of Swiss-Prot proteins           
 567   ProtoNet            Hierarchical clustering of Swiss-Prot proteins               
 217   SBASE               Protein domain sequences and tools                           
 867   SIMAP               Similarity matrix of proteins: precomputed similarity data   
1010   SISYPHUS            Structural alignments for proteins with non-trivial relationships
 218   SMART               Simple modular architecture research tool: signalling, extracellular
                              and chromatin-associated protein domains
219    SUPFAM                 Grouping of sequence families into superfamilies        
199    TIGRFAMs               TIGR protein families adapted for functional annotation 

       3.6. Databases of individual protein families
157    ABCdb                  Archaeal and bacterial ABC transporter database         
156    Aminoacyl-tRNA         Aminoacyl-tRNA synthetase database                      
       synthetases database
1045   Animal Toxin DB        Database of animal toxins                               
 412   ARAMEMNON              Arabidopsis thaliana membrane proteins and transporters 
1166   BACTIBASE              Database of bacteriocin natural antimicrobial peptides  
 158   BacTregulators         Transcriptional regulators of AraC and TetR families              No longer maintained
 976   BANMOKI                Database of bacterial nucleoside monophosphate kinases  
1057   ChromDB                Chromatin-associated proteins in a broad range of organisms
 923   cpnDB                  Chaperonin database                                     
1154   CREMOFAC               Database of chromatin remodeling factors                
 364   CSDBase                Cold Shock Domain database                              
1168   CyMoBase               Cytoskeletal and motor proteins database                
1065   DB-PABP                Experimentally characterized polyanion-binding proteins 
 658   DCCP                   Database of Copper-Chelating Proteins                   
 945   Defensins              Antimicrobial peptides of the defensin family           
160    DExH/D Family DB       DEAD-box, DEAH-box and DExH-box proteins                
892    DSD                    Database of dehydrogenase stereospecificities           
161    Endogenous GPCR List   G protein-coupled receptors; expression in cell lines   
814    EROP-Moscow            Database of Endogenous Regulatory OligoPeptides         
162    ESTHER                 Esterases and other alpha/beta hydrolase enzymes        
 164   FUNPEP                 Low-complexity peptides capable of forming amyloid plaque
 166   GPCRDB                 G protein-coupled receptors database                    
 679   gpDB                   G-protein database: G-proteins and their interaction with GPCRs
1085   Heme Protein DB        Heme protein structure, heme type, axial ligands, and heme
                              protein reduction potential (Em) values
167    Histone Database       Histone fold sequences and structures                   
365    HIV RT and Protease    HIV reverse transcriptase and protease sequences        
       Sequence Database
169    Homeobox Page          Homeobox proteins, classification, and evolution        
170    Homeodomain            Homeodomain sequences, structures, and related genetic and
       Resource                  genomic information
174    InBase                    Inteins (protein splicing elements) database: properties,
                                 sequences, bibliography
518    KinG                      Kinases in Genomes: Ser/Thr/Tyr kinases encoded in the  
                                 completely sequenced genomes
519    Knottin database          Database of knottins, small proteins with an unusual "disulfide
                                 through disulfide" knot
176    LGICdb                    Ligand-gated ion channel subunit sequences database     
 368   Lipase Engineering DB     Sequence, structure and function of lipases and esterases
 524   LOX-DB                    Mammalian, invertebrate, plant and fungal lipoxygenases 
 177   MEROPS                    Database of proteolytic enzymes (peptidases)            
1105   NORINE                    Database of nonribosomal peptides                       
 546   NucleaRDB                 Nuclear receptor superfamily                            
 184   Olfactory Receptor DB     Sequences for olfactory receptor-like molecules         
 186   Peptaibol                 Peptaibol (antibiotic peptide) sequences                
 560   PhytoProt                 Clusters of (predicted) plant proteins                  
 189   PLANT-PIs                 Plant protease inhibitors                               
 371   PlantsP/PlantsT           Plant proteins involved in phosphorylation and transport
 759   PLPMDB                    Pyridoxal-5'-phosphate dependent enzymes mutations      
 609   ProLysED                  Database of bacterial protease systems                  
 192   Prolysis                  Proteases and natural and synthetic protease inhibitors 
 188   Protein kinase resource   Protein kinase resource: sequences, enzymology, genetics and
                                 molecular and structural properties
 224   REBASE                    Restriction enzymes and associated methylases           
 195   RNAse P Database          Ribonuclease P sequences, alignments and structures     
 901   RNRdb                     Ribonucleotide reductase database                       
 573   RPG                       Ribosomal Protein Gene database                         
 575   RTKdb                     Receptor Tyrosine Kinase database                       
 372   SDAP                      Structural database of allergenic proteins and food allergens
1131   SelenoDB                  Database of selenoprotein genes, proteins and SECIS elements
 196   SENTRA                    Sensory signal transduction proteins                    
 373   SEVENS                    7-transmembrane helix receptors (G-protein-coupled)     
1137   Telomerase database       Sequences and structures of the RNA and protein subunits of
                                 telomerase, mutations of telomerase components
311    TransportDB               Predicted membrane transporters in complete genomes, classified
                                 according to the TC classification system
399    VKCDB                     Voltage-gated K Channel Database                        
202    Wnt Database              Wnt proteins and phenotypes                             
       4. Structure Databases

       4.1. Small molecules
 402   AANT                   Amino Acid - Nucleotide interaction database             
 646   ChEBI                  Chemical entities of biological interest                 
1024   ChemBank               Structures and biological activities of small organic molecules
1023   ChemDB                 3D structures and properties of small molecules          
 261   CSD                    Cambridge Structural Database                            
 360   Het-PDB Navi           Hetero-atoms in protein structures                       
 265   HIC-Up                 Hetero-compound Information Centre - Uppsala             
 111   Klotho                 Collection and categorization of biological compounds    
 113   LIGAND                 Chemical compounds and reactions in biological pathways  
 615   PDB-Ligand             3D structures of small molecules bound to proteins and nucleic
 735   PubChem                Structures and biological activities of small organic molecules
1127   R.E.DD.B.              RESP and ESP atomic charges and force field libraries for small
                              molecules and molecular fragments
       4.2. Carbohydrates
 977   BCSDB/Glycoscience     Bacterial Carbohydrate Structure DataBase                
 429   CarbBank               CCSD - Complex Carbohydrate Structure Database           
 652   CSS                    Carbohydrate Structure Suite: carbohydrate 3D structures 
 486   Glycan                 Carbohydrate database, part of the KEGG system           
1080   Glycoconjugate Data    Annotated structures of glycan molecules                 
988    GlycoMaps DB           Conformational maps of disaccharides                     
292    GlycoSuiteDB           N- and O-linked glycan structures and biological sources 
535    Monosaccharide         Space filling Fischer projections of monosaccharides     
300    SWEET-DB               Annotated carbohydrate structure and substance information
       4.3. Nucleic acid structure
1082   Greglist               G-quadruplex motifs and potentially G-quadruplex regulated genes
1090   ITS2                   Predicted structures of internal transcribed spacer 2 (ITS2)       http://its2.bioapps.biozentrum.uni-
 272   NDB                    Nucleic acid-containing structures                       
 273   NTDB                   Thermodynamic data for nucleic acids                     
1126   QuadBase               G-quadruplex motifs in the promoters of human, chimpanzee, rat,
                              mouse and bacterial genes
1129   RNA FRABASE            Database of 3D RNA fragments within known RNA structures    
 387   RNABase                RNA-containing structures from PDB and NDB                  
1130   RNAJunction            RNA structural elements: helical junctions, internal loops, bulges
                              and loop-loop interactions
908    SARS-CoV RNA SSS       Predicted secondary structures of SARS coronavirus RNA      
283    SCOR                   Structural classification of RNA: RNA motifs by structure, function
                              and tertiary interactions
       4.4. Protein structure
401    3D-Genomics            Structural annotations for complete proteomes               
633    3DID                   3D interacting domains                                      
413    ArchDB                 Automated classification of protein loop structures         
255    ASTRAL                 Sequences of domains of known structure, selected subsets and
                              sequence-structure correspondences
1047   AutoPSI                Automated structural classification of protein sequences    
 257   BioMagResBank          NMR spectroscopic data from proteins, peptides, and nucleic acids
 384   CADB                   Conformational Angles DataBase of Proteins                  
 258   CATH                   Protein domain structures database                          
 259   CE                     Combinatorial Extension method to compute and review 3D     
                              protein structure alignments
 260   CKAAPs DB              Conserved Key Amino Acid Positions Database                           No longer maintained
 882   CoC Central            Universally conserved residues in protein folds             
1059   ColiSNP                Mapping non-synonymous SNPs on protein structures           
 883   Columba                Annotation of protein structures from the PDB               
 442   Dali database          Fold classification based on structural alignment of proteins
1169   DBAli                  Database of structure alignments                            
 385   Decoys-R-Us            Computer-generated protein conformations based on sequence  
447    DisProt                Database of Protein Disorder                                
809    DMAPS                  Database of multiple alignments for protein structures      
264    DSDBASE                Disulfide Database                                          
386    DSMM                   A Database of Simulated Molecular Motions                   
456    E-MSD                  EBI-Macromolecular Structure Database                       
818    FSN                    Flexible structural neighborhood, structural neighbors of proteins
                              identified by FATCAT tool                                             cgi/cgi/struct_neibor/
469    FSSP                                                                                         Superseded by the Dali database, no. 442
472    Gene3D                 Precalculated structural assignments for whole genomes      
489    Genomic Threading DB   Structural annotations of complete genomes                  
322   GTOP                      Protein fold predictions from genome sequences             
498   HOMSTRAD                  Homologous structure alignment database: curated structure-
                                based alignments for protein families
267   IMB Jena Image Library    Visualization and analysis of 3D biopolymer structures     
502   IMGT/3Dstructure-DB       3D structures of Immunoglobulins, T cell receptors, and MHC
829   IMOTdb                    Spatially interacting motifs in proteins                   
269   LPFC                      Library of protein family core structures                  
270   MMDB                      All experimentally-determined 3D structures, linked to NCBI Entrez
331   ModBase                   Annotated comparative protein structure models             
262   MolMovDB                  Database of Macromolecular Movements                       
107   MPID                      MHC-Peptide Interaction Database                           
275   PASS2                     Structural motifs of protein superfamilies                 
276   PDB                       Protein Data Bank: all known protein structures            
619   PDB_TM                    Transmembrane proteins with known 3D structure             
277   PDB-REPRDB                Representative protein chains, based on PDB entries        
278   PDBsum                    Summaries and analyses of PDB structures                   
557   PepConfDB                 Database of peptide conformations                          
719   PFD                       Protein Folding Database : Experimental data on protein folding
855   PMDB                      3D protein models obtained from structure predictions      
281   RESID                     Post-translational modifications of proteins               
740   S4                        Structure-based Sequence Alignments of SCOP Superfamilies  
282   SCOP                      Structural classification of proteins                      
863   SCOPPI                    Structural classification of protein-protein interfaces    
284   SLoop                     Classification of protein loops                            
530   SSToSS                    Sequence-Structural Templates of Single-member Superfamilies
785   STING Report              Amino acid properties in proteins of known structure       
583   Structure Superposition   Pairwise superpositions of 115 TIM-barrel structures       
285   SUPERFAMILY               Assignments of proteins to structural superfamilies        
584   SURFACE                   Surface residues and functions annotated, compared and     
                                evaluated: a database of protein surface patches
585   SWISS-MODEL               3D protein structure models generated by automated homology
      Repository                modeling using SWISS-MODEL
764   TargetDB                  Target data from worldwide structural genomics projects    
938   TMBETA-GENOME             Beta-barrel membrane proteins encoded in various genomes   
941   TOPOFIT-DB                Protein structural alignments based on the TOPOFIT method  
310   TOPS                      Topology Of Protein Structures                             
       5. Genomics Databases (non-human)

       5.1. Genome annotation terms, ontologies and nomenclature
 915   BioThesaurus         A collection of gene/protein names and associated sequences
1075   FunSimMat            Gene Ontology-based functional similarity values for proteins and
                            protein families
487    GO                   Gene ontology consortium database                         
389    GOA                  Gene Ontology Annotation                                  
939    GOPaD                Gene Ontology Partition Database                          
 73    HGNC Database        The HUGO Gene Nomenclature Database (formerly Genew)      
513    IUBMB Nomenclature   Nomenclature of enzymes, membrane transporters, electron  
       database             transport proteins and other proteins
514    IUPAC Nomenclature   Nomenclature of biochemical and organic compounds approved
       database             by the IUBMB-IUPAC Joint Commission
515    IUPHAR-RD            International Union of Pharmacology recommendations on    
                            receptor nomenclature and drug classification
926    Plant Ontology DB    Controlled vocabulary of plant structures and growth stages
358    SOURCE               Functional genomics resource for human, mouse and rat     
906    TreeBase             Phylogenetic trees and the data matrices used to generate them
317    UMLS                 Unified medical language system                                     Requires user registration
       5.2. Taxonomy and identification
1018   GeneTrees            Pre-compiled alignments and gene phylogenies for a variety of
                            taxonomic groups
  78   ICB                  gyrB database for identification of bacteria              
1088   IDBD                 Infectious Disease Biomarker Database                     
 297   NCBI Taxonomy        Names of all organisms that are represented in GenBank    
       Browser                                                                                  e.html
 299   RIDOM                Ribosomal Differentiation of Medical Microorganisms       
1135   SuperCAT             Database for multilocus sequence typing analysis of the Bacillus
                            cereus group of bacteria
301    Tree of Life         Information on phylogeny and biodiversity                 
965    VNTR Locus DB        Bacterial Variable Number Tandem Repeat locus database    
       5.3. General genomics databases
641    BacMap               Picture atlas of annotated bacterial genomes              
650    CoGenT++             Complete genome tracking: Predicted peptides from fully   
                            sequenced genomes
 445   DEG                  Database of Essential Genes                             
1172   diArk                Database of eukaryotic sequencing projects              
 451   EBI Genomes          EBI’s collection of databases for the analysis of complete and
                            unfinished viral, pro- and eukaryotic genomes
458    Entrez Genomes       NCBI’s collection of databases for the analysis of complete and
                            unfinished viral, pro- and eukaryotic genomes                     nome
461    ERGO-Light           Integrated biochemical data on 10 bacterial genomes: Publicly-
                            available portion of the ERGO database
 674   GenDiS               Genomic distribution of protein structural superfamilies
 327   GeneNest             Gene indices of human, mouse, zebrafish, etc.           
1077   GenoList             An integrated environment for comparative analysis of microbial
484    Genome Information   DDBJ’s collection of genome databases                   
678    Genome Reviews       Integrated view of complete genomes                     
916    Genome Project DB    NCBI's database of large-scale genome sequencing projects
75     GOLD                 Genomes online database: a listing of completed and ongoing
                            genome projects
830    HOINVGEN             Homologous invertebrate genes                                     http://pbil.univ-
690    Inparanoid           Database of eukaryotic orthologs                        
223    Integr8              Functional classification of proteins in whole genomes  
777    KaryotypeDB          Karyotype and chromosome data for animal and plant species
112    KEGG                 Kyoto Encyclopedia of Genes and Genomes: databases on genes,
                            proteins, and metabolic pathways
 528   MBGD                 Microbial genome database for comparative analysis      
 114   MetaCyc              Metabolic pathways and enzymes from various organisms   
1103   Narcisse             Conserved syntenies for various animal, plant and bacterial
 703   NegProt              Negative Proteome: A tool for comparison of complete proteomes
1040   NMPDR                Database for functional annotation and comparative analysis of
                            microbial genomes
1106   OPTIC                Orthologous and Paralogous Transcripts in Clades        
 549   ORFanage             Orphan ORFs (ORFs with no homologs) in microbial genomes          No longer maintained
1108   OrthoDB              An hierarchical catalog of orthologous proteins in metazoa
 847   OrthoMCL             Orthologous protein clusters from multiple genomes      
 715   PartiGeneDB          Assembled partial genomes for ~250 eukaryotic organisms 
 354   PEDANT               Results of an automated analysis of genomic sequences   
 377   PEP                  Predictions for Entire Proteomes                        
1113   PhylomeDB                Experimentally validated and predicted serine phosphorylation sites
                                in Arabidopsis thaliana
118    PUMA2                    Metabolic analysis of complete microbial genomes            
582    STRING                   Predicted functional associations between proteins          
 66    TIGR Comprehensive       Various data on complete microbial genomes: Uniform annotation,
       Microbial Resource       properties of DNA and predicted proteins                              scripts/CMR2/CMRHomePage.spl
  5    TIGR Gene Indices        Organism-specific databases of EST and gene sequences       
 99    TIGR Microbial DB        A list of microbial genome sequencing projects                        No longer maintained
877    VBI Microbial Database   Virginia Bioinformatics Institute microbial database        
       5.4. Viral genome databases
1051   BioHealthBase            Host-pathogen interactions of influenza virus               
1061   CoVDB                    Database of coronavirus genes and genomes                   
 810   DPVweb                   Descriptions of plant viruses                               
1034   euHCVdb                  European Hepatitis C Virus database                         
 492   HCV Database             Hepatitis C Virus (HCV) Sequence Database                   
 473   HCVdb                    Hepatitis C Virus Database                                  
 972   HepSeq                   Epidemiological, clinical, and sequence data on the Hepatitis B
                                virus                                                                 hepatitis_open/main.php
495    HERVd                    Human Endogenous Retrovirus database                        
497    HIV Drug Resistance      HIV mutations that confer resistance to anti-HIV drugs      
168    HIV Molecular            HIV epitopes                                                
       Immunology Database
990    HIV Positive Selection   Positively selected mutations in HIV-1 protease and reverse 
       Mutation Database        transcriptase
909    Influenza Virus          Protein and nucleotide sequences of the influenza virus     
993    IVDB                     Influenza Virus Database : Annotated sequences and geographic
                                distribution of the influenza virus
602    NCBI Viral Genomes       Viral genome resource at NCBI                               
725             Poxvirus genomic sequences and gene annotation              
750    T4-like genome DB        Sequences of T4-like bacteriophages from various sources    
201    VIDA                     Homologous viral protein families database                  
761    VIPERdb                  Virus particle explorer: Virus capsid structures            
798    Viral Bioinformatics     Virus orthologous genes, gene families and genomes          
       Resource Center
 397   VirGen                    Curated database for complete viral genome sequences     
1039   ViTa                      microRNAs targets of the influenza virus                 
       5.5. Prokaryotic genome databases
       5.5.1. General
1044   AlterORF                  Database of alternate open reading frames                
 641   BacMap                    Picture atlas of annotated bacterial genomes             
 884   Comparative               DNA walks, nucleotide skews and other biometric measures of
       Genometrics               prokaryotic genomes
70     EMGlib                    Enhanced microbial genomes library: Completely sequenced 
                                 genomes of unicellular organisms
 328   GeneDB                    Curated database for various Sanger-sequenced genomes    
 611   Genome Atlas              DNA structural properties of sequenced genomes           
1084   HEG-DB                    Predicted highly expressed genes in prokaryotic genomes  
 352   HGT-DB                    Horizontal Gene Transfer-DataBase                        
 828   IMG                       Comparative analysis of microbial genomes sequenced at the DOE
                                 Joint Genome Institute
1089   IMG/M                     A data management and analysis system for metagenomes    
 826   Interrupted coding        Interrupted coding sequences: frameshifts, stop codons,  
       sequences DB              sequencing errors in microbial genomes
837    MeGX                      Marine ecological genomix: genomics and metagenomics of marine
 614   MetaGrowth                Growth requirements of bacterial pathogens               
 959   MiST                      Microbial Signal Transduction database                   
 720   PGTdb                     Prokaryotic growth temperature database                  
  43   RRNDB                     rRNA operon numbers in various prokaryotes               
1160   Roundup                   Repository of orthologs and corresponding evolutionary distances
 866   SIDDBase                  Stress-induced DNA duplex destabilization profiles of complete
                                 microbial genomes                                                  ase/
426    xBase                     A family of group-specific bacterial genome databases, includes
                                 coliBASE, CampyDB, ClostriDB, MycoDB, PseudoDB and others
       5.5.2. Escherichia coli
415    ASAP                      A Systematic Annotation Package                          
428    CCDB                      CyberCell Database                                       
436    coliBase                  Database for E. coli, Salmonella and Shigella            
437    Colibri                                                                            
623    EchoBASE                  Post-genomic studies of Escherichia coli                 
108    EcoCyc                    E. coli K12 genes, pathways, transporters, and gene regulation
  69   EcoGene                    Sequence and literature data on E. coli genes and proteins  
1070   ERIC                       Enteropathogen Resource Integration Center                  
 462   Essential genes in E.      A list of genes essential for viability of E. coli          
482    GenoBase                   Functional genomic aAnalysis of E. coli in Japan            
165    GenProtEC                  E. coli K12 genome and proteome database                    
       5.5.3. Bacillus subtilis
424    BSORF                      Bacillus subtilis Open Reading Frames                       
 31    DBTBS                      Bacillus subtilis promoters and transcription factors       
 89    NRSub                      Non-redundant Bacillus subtilis database at U. Lyon         
 96    SubtiList                  Bacillus subtilis genome database at Institut Pasteur       
       5.5.4. Other bacteria
1153   BuchneraBase               Genomic database for the pea aphid symbiont Buchnera sp. APS
 426   CampyDB                    Campylobacter Database                                                Incoroporated into xBase, no. 426
 648   CIDB                       Chlamydia Interactive Database: Gene expression data        
 433   ClostriDB                  Clostridium Database                                                  Incoroporated into xBase, no. 426
1167   CoryneRegNet               Corynebacterial transcription factors                       
  68   CyanoBase                  Cyanobacterial genomes                                      
 834   LEGER                      Post-genome research of Listeria                            
 521   LeptoList                  Leptospira interrogans genome                               
 534   MolliGen                   Genomic data on mollicutes                                  
 896   MtbRegList                 Mycobacterium tuberculosis gene regulation                  
 996   MvirDB                     Protein toxins, virulence factors, and antibiotic resistance genes
 944   PAIDB                      Pathogenicity islands in bacterial genomes                  
1000   PATRIC                     PathoSystems Resource Integration Center                    
 555   PEC                        Profiling of E. coli Chromosome                             
 720   PGTdb                      Prokaryotic growth temperature database                     
 733   PseudoCAP                  Pseudomonas aeruginosa community genome annotation project  
 947   RegTransBase               Manually curated database of regulatory interactions in prokaryotes
  94   RsGDB                      Rhodobacter sphaeroides genome                              
 865   ShiBase                    Shigella database                                           
 760   VFDB                       Virulence Factors of pathogenic bacteria                    
1017   xanthusBase                Genome of the social bacterium Myxococcus xanthus           
       5.5.5. Archaea
964    Sulfolobus Database        Comparative genomics of Sulfolobus species                  
876    UCSC Archaeal              Pyrococcus furiosus genome browser                          
       Genome Browser
       5.6. Unicellular eukaryotes genome databases
 969   ApiDB                   Unified resource for various apicomplexan species        
 409   ApiDots                 EST sequences from various Apicomplexan parasites        
 983   Comparasite             Database for comparative study of parasite cDNAs         
 439   CryptoDB                Cryptosporidium database                                 
 662   Diatom EST DB           ESTs from diatom algae Thalassiosira and Phaeodactylum   
 446   DictyBase               Universal resource for Dictyostelium discoideum          
  72   Full-Malaria            Full-length cDNA library from erythrocytic-stage Plasmodium
 917   ParameciumDB            Paramecium genome sequencing project                     
  91   PlasmoDB                Plasmodium genome database                               
1124   ProtozoaDB              Comparative analysis of protozoan genomes                
 912   TBestDB                 Taxonomically broad EST database: protist ESTs           
 586   TcruziDB                Trypanosoma cruzi genome database                        
 359   ToxoDB                  Toxoplasma gondii genome database                        
 910   U-genome                Genome organization in unicellular eukaryotes            
       5.7. Fungi
1056   CFGP                    Comparative Fungal Genomics Platform                     
 955   Fungal Genome Size      Genome sizes of various fungi                            
       5.7.1. Yeasts
635    AGD                     Ashbya gossypii genome database                          
617    CandidaDB               Candida albicans genome database                         
645    Candida Genome          Candida albicans genome database                         
441    CYGD                    MIPS Comprehensive yeast genome database                 
483    Génolevures             A comparison of S. cerevisiae and 14 other yeast species 
841    Mpact                   Yeast protein-protein interaction data                   
730    PROPHECY                Profiling of phenotypic characteristics in yeast         
576    SCMD                    Saccharomyces cerevisiae morphological database: micrographs of
                               budding yeast mutants
577    SCPD                    Saccharomyces cerevisiae promoter database               
357    SGD                     Saccharomyces genome database                            
 25    TRIPLES                 Transposon-insertion phenotypes, localization, and expression in
306    YDPM                    Yeast deletion project and mitochondria database                   http://www-
342    Yeast Intron Database   Ares lab database of splicesomal introns in S. cerevisiae
792   YEASTRACT               Yeast search for transcriptional regulators and consensus tracking
254   Yeast snoRNA DB         Yeast small nucleolar RNAs                                 
791   YGOB                    Yeast gene order browser                                   
307   yMGV                    Yeast microarray global viewer                             
531   YMPD                    Yeast mitochondrial protein database                       
763   YRC PDR                 Yeast resource center public data repository               
      5.7.2. Other fungi
425   CADRE                   Central Aspergillus data repository                        
435   COGEME                  Phytopathogenic fungi and oomycete EST database            
815   FGDB                    MIPS Fusarium graminearum genome database                  
525   Magnaporthe grisea DB   Magnaporthe grisea Database                                
533   MNCDB                   MIPS Neurospora crassa database                            
708   OGD                     Oomycete Genomics Database: ESTs and annotation            
852   PHI-base                Genes affecting fungal pathogen-host interactions          
 98   Phytophthora Functio-   ESTs and expression data from P. infestans and P. sojae    
      nal Genomics DB
      5.8. Invertebrates
      5.8.1. Caenorhabditis elegans
430   C. elegans Project      Genome sequencing data at the Sanger Institute             
238   Intronerator            Introns and splicing in C. elegans and C. briggsae         
570   RNAiDB                  RNAi phenotypic analysis of C. elegans genes               
864   SGCEdb                  Structural genomics of C. elegans                                    No longer maintained
304   WorfDB                  C. elegans ORFeome                                         
 51   WormBase                Data repository for C. elegans and C. briggsae: curated genome
                              annotation, genetic and physical maps, pathways
961   WormBook                Peer-reviewed chapters on the biology of C. elegans        
      5.8.2. Drosophila melanogaster
774   DPDB                    Drosophila polymorphism database                           
928   DroID                   Drosophila gene and protein interaction data               
449   Drosophila microarray   Canadian Drosophila microarray centre                      
924   DroSpeGe                Drosophila Species Genomes                                 
816   FLIGHT                  Drosophila phenotypes, gene expression and protein interactions
 71   FlyBase                 Drosophila sequences and genomic information               
767   FlyBrain                Database of the Drosophila nervous system                  
 670   FlyMine                Integration of insect genomic and proteomic data        
 817   FlyRNAi DRSC           Genome-wide RNAi analysis data in Drosophila            
1073   FLYSNP                 Single nucleotide polymorphism data for Drosophila melanogaster
1158   FlyTF                  Drosophila Transcription Factors                        
 467   FlyTrap                Drosophila mutants created using protein trap strategy  
  14   FlyView                Drosophila development and genetics                     
 471   GadFly                 Genome annotation database of Drosophila                
 677   GeniSys                Enhancer- and promoter-inserted mutants of Drosophila   
 989   GenomeRNAi             Cell-based RNAi phenotypes database                     
   8   Homophila              Drosophila homologs of human disease genes              
 509   InterActive Fly        Drosophila genes and their roles in development         
1128   REDfly                 Regulatory modules and transcription factor binding sites in
       5.8.3. Other invertebrates
  63   ACeDB                  C. elegans, S. pombe, and human genomic information     
1152   AphidBase              Genomic database for the pea aphid (Acyrthosiphon pisum)
 410   AppaDB                 Database on the nematode Pristionchus pacificus         
 643   BeetleBase             Genome database of the beetle Tribolium castaneum       
1052   ButterflyBase          Genomics of butterflies (Lepidoptera)                   
 649   Ciliate IES-MDS Db     Macro- and micronuclear genes in spirotrichous ciliates 
 434   CnidBase               Cnidarian evolution and gene expression database        
 653   CuticleDB              Structural proteins of Arthropod cuticle                
 698   LumbriBASE             ESTs of the earthworm Lumbricus rubellus                
 543           Parasitic nematode sequencing project                   
 544   NEMBASE                Nematode sequence and functional data database          
 726   PPNEMA                 Plant-parasitic nematode rRNAs                          
1006       Genome data of the nematode <I>Pristionchus pacificus</I>
1161   Sebida                 Sex bias in insect gene expression database             
 743   SilkDB                 Silkworm Bombyx mori ESTs, mutants, photographs         
 744   SilkSatDb              A microsatellite database of the silkworm Bombyx mori   
1133   SmedGD                 The Schmidtea mediterranea genome database              
 747   SpodoBase              Genomics of the butterfly Spodoptera frugiperda         
 871   StellaBase             Nematostella vectensis (sea anemone) genome             
 873   Tetrahymena Genome     Tetrahymena thermophila genome database                 
1031   VectorBase             Invertebrate Vectors of Human Pathogens                 
 925   wFleaBase              Daphnia Water Flea Genome Database                      
       6. Metabolic Enzymes and Pathways; Signaling Pathways
898    Pathguide               A listing of pathway, signal transduction and protein-protein
                               interaction databases
       6.1. Enzymes and enzyme nomenclature
421    BRENDA                  Enzyme names and biochemical properties                  
109    ENZYME                  Enzyme nomenclature and properties                       
459    Enzyme Nomenclature     IUBMB Nomenclature Committee recommendations             
613    EzCatDB                 Enzyme Catalytic Mechanism Database                      
716    FCP                     Functional coverage of the proteome by structures        
508    IntEnz                  Integrated enzyme database and enzyme nomenclature       
893    MACiE                   Mechanism, annotation and classification in enzymes: enzyme
                               reaction mechanisms
 998   ORENZA                  ORphan ENZymes database                                  
 727   PRECISE                 Predicted and Consensus Interaction Sites in Enzymes     
1121   PROCOGNATE              Protein cognate ligands for the domains in enzyme structures
758    SCOPEC                  Mapping of catalytic function to domain structure        
772    TECRdb                  Thermodynamics of enzyme-catalyzed reactions             
       6.2. Metabolic pathways
419    BioCarta                Online maps of metabolic and signaling pathways          
420    BioCyc                  Pathway/genome databases for many bacteria               
423    Biodegradative Strain   Microorganisms that can degrade aromatic and other organic
       Database                compounds
644    BioSilico               Integrated access to various metabolic databases         
991    HMDB                    The Human Metabolome Database: Curated human metabolite and
                               metabolism data
112    KEGG Pathway            Metabolic and regulatory pathways in complete genomes    
835    Lipid MAPS              Lipid metabolites and pathways strategy                  
114    MetaCyc                 Metabolic pathways and enzymes from various organisms    
115    PathDB                  Biochemical pathways, compounds and metabolism                     No longer maintained
612    Reactome                Database of metabolic and signaling pathways             
953    SYSTOMONAS              SYSTems biology of pseudOMONAS                           
117    UM-BBD                  University of Minnesota biocatalysis and biodegradation database
       6.3. Protein-protein Interactions
633    3DID                     3D interacting domains: Domain-domain interactions in proteins
                                 with known 3D structures
1042   3D-Interologs             Protein-protein interactions in various evolutionary lineages 
 796   AffinDB                   Affinity data for protein-ligand complexes                    
 405   aMAZE                     A system for the annotation, management, and analysis of      
                                 biochemical and signalling pathway networks
1046   AtPID                     Arabidopsis thaliana Protein Interactome Database             
1048            Protein interaction database for E. coli                      
 103   BIND                      Biomolecular interaction network database                               No longer free for all
1049   Binding MOAD              Binding Mother of All Databases: protein-ligand crystal structures
 800   BioGRID                   Genetic and physical interactions in yeast, worm and fly      
 422   BRITE                     Biomolecular Relations in Information Transmission and        
980    CellCircuits              Molecular network models: from pairwise molecular interactions to
                                 whole pathways
1060   CORUM                     Experimentally verified mammalian protein complexes           
 946   CutDB                     Community annotation resource for proteases, their substrates 
                                 and cleavage sites
 659   DDIB                      Database of domain interactions and binding                   
1066   DIMA                      Domain interaction map: experimental data and predictions on  
                                 protein domain interactions
104    DIP                       Database of interacting proteins: Experimentally-determined   
                                 protein-protein interactions
1155   Dockground                Protein-protein interfaces in co-crystallized protein structures
1067   DOMINE                    Known and predicted protein domain interactions in PDB entries
1033   DOMINO                    Domain peptide interactions                                   
 105   DRC                       Database of ribosomal crosslinks                                        http://www.mpimg-berlin-
1086   HotSprint                 Hot spots (functionally and structurally important residues) in
                                 protein interfaces
664    hp-DPI                    Database of protein interactions in Helicobacter pylori       
688    HPID                      Human protein interaction database                            
897    I2D                       Interologous Interaction Database: Predicted protein-protein  
                                 interactions in humans
 507   IntAct                    Protein-protein interaction data                              
 770   Inter-Chain Beta-Sheets   Protein interactions mediated by interchain beta-sheet formation
 510   InterDom                  Putative protein domain interactions                          
 138   KDBI                      Kinetic data of bio-molecular interactions                    
1091   LigAsite                  Biologically relevant binding sites in proteins with known structures
 942   MiMI                      Michigan Molecular Interactions: Protein-protein interactions 
1032   MINT                      Molecular INTeraction                                         
 897   OPHID                    Online predicted human interaction database                         Superseded by I2D (no. 897)
 718   PDZBase                  Protein-protein interactions involving PDZ domains        
1111   PepCyber:P~Pep           Human protein interactions mediated by phosphoprotein-binding
773    PINdb                    Proteins interacting in nucleus (human and yeast)         
748    POINT                    Prediction of human protein-protein interactome           
729    ProNIT                   Protein-nucleic acid interactions                         
 943   PROTCOM                  3D structures of two-chain protein complexes              
 616   PSIbase                  Interaction of proteins with known 3D structures          
1012   SNAPPI                   Structures, iNterfaces and Alignments for Protein-Protein 
                                Interactions                                                        s.jsp
1134   STITCH                   Search Tool for Interactions of Chemicals                 
 749   Structurally conserved   Interacting residues in protein-protein interfaces in PDB 
       interfaces                                                                                   ACES.html
1138   The Cell Cycle DB        Genes and proteins involved in human and yeast cell cycle 
 960   UniHI                    Unified Human Interactome: human protein-protein interactions
       6.4. Signaling pathways
 419   BioCarta                 Online maps of metabolic and signaling pathways           
 794   Cyclonet                 Database on cell cycle regulation                         
 890   EndoNet                  Information on endocrine networks                         
1038   Hedgehog signalling      Resources and annotations of the Hedgehog signaling pathway
1104   NetworKIN                Network approach to human protein kinases and their substrates
1112   PhosPhAt                 Arabidopsis Protein Phosphorylation Site Database         
1175   PRRDB                    Pattern recognition receptors and their ligands           
 858   pSTIING                  Protein signalling, transcriptional interactions and inflammation
                                networks gateway
 571   ROSPath                  Reactive oxygen species (ROS) signaling pathway           
 395   STCDB                    Signal Transduction Classification Database               
1142   UCSD-Nature Signaling    Expert-authored and peer-reviewed information on mammalian
       Gateway                  proteins involved in cellular signaling
       7. Human and other Vertebrate Genomes
       7.1. Model organisms, comparative genomics
879    ABA                     Ascidian body atlas: digital 3D model of ascidian development
974    AgBase                  GO annotations for agriculturally important plants and animals
 26    AllGenes                Human and mouse gene, transcript and protein annotation
957    Animal Genome Size      Genome sizes of vertebrates and invertebrates          
 975   AnimalQTLdb             Quantitative trait loci in livestock animals           
  65   ArkDB                   Genome databases for farm and other animals            
  12   BodyMap                 Human and mouse gene expression data                   
 881   BodyMap-Xs              Cross-species comparison of vertebrate gene expression 
 647   ChickVD                 Sequence variation in the chicken genome               
 286   Cre Transgenic DB       Cre transgenic mouse lines with links to publications  
 337   CORG                    COmparative Regulatory Genomics: conserved non-coding blocks
 808   DBTGR                   Database of tunicate Ciona gene regulation             
 660   DED                     Database of evolutionary distances                               No longer maintained
  20   Edinburgh Mouse Atlas   Digital atlas of mouse embryonic development           
 453   EGO                     Eukaryotic Gene Orthologs                              
  27   Ensembl                 Annotated information on eukaryotic genomes            
 396   euGenes                 Genomic Information for Eukaryotic Organisms           
1071   EuroPhenome             Large-scale phenotyping of knockout mouse lines        
 673   GALA                    Genomic alignment, annotation and experimental results 
1076   Gallus Gbrowse          Genomic information on chicken and other avian species 
1173   GEISHA                  Gallus expression in situ hybridization analysis       
  15   GXD                     Mouse Gene Expression Database                         
605    HomoloGene              Automatically detected homologous genes in complete eukaryotic
                               genomes                                                          mologene
  8    Homophila               Drosophila homologs of human disease genes             
400    KOG                     Eukaryotic Orthologous Groups of proteins              
952    MamPol                  Mammalia Polymorphism Database                         
839    MFunGD                  MIPS mouse functional genomics database                
 87    Mouse Genome DB         Formerly mouse genome database                         
995    Mouse Phenome DB        phenotypic and genotypic data from inbred strains of mice
537    Mouse SAGE              SAGE libraries from various mouse tissues and cell lines
540    Mouse Transposon        Mouse Transposon Insertion Database                    
       Insertion Database
152    Mouse Tumor Biology     Tumor types, genes, classification, incidence, pathology  
598    Non-Human Genome        Segmental duplications in mouse, dog and chicken genomes  
       Segmental Duplication
 548   OMIA                    Online Mendelian Inheritance in Animals                   
 553   ParaDB                  Paralogy mapping in human genomes                         
 554   PathBase                European mutant mice histopathology database: images      
1110   PBmice                  piggyBac transposon insertions in the mouse genome.       
 556   PEDE                    Pig Expression Data Explorer: Pig cDNA libraries and ESTs 
 936   PigGIS                  Pig genome mapping, genes and ESTs                        
  93   Rat Genome Database     Rat genetic and genomic data                              
 625   RatMap                  Rat genome tools and data                                 
 574   RTCGD                   Retroviral Tagged Cancer Gene Database                    
1164   SPEED                   Searchable prototype experimental evolutionary database   
 751   TAED                    The Adaptive Evolution Database: plant and chordate gene families
 875   TreeFam                 Tree families database: phylogenetic trees of animal genes
1144   UniTrap                 Unambiguous insertions in the same subgenic regions of annotated
                               mouse genes
1145   UTGB/medaka             University of Tokyo Genome Browser of medaka fish (Oryzias
                               latipes) genomic data
784    VEGA                    Vertebrate genome annotation: a repository for manual annotation
                               of finished vertebrate genome sequences
1150   XenBase                 Xenopus genomics resource                                 
 101   ZFIN                    Zebrafish information network                             
       7.2. Human genome databases, maps and viewers
985    ENCODE Project          Encyclopedia of DNA Elements, all functional elements in the
                               human genome
 56    GDB                     Human genes and genomic maps                              
 35    Gene Resource Locator   Alignment of ESTs with finished human sequence                      No longer maintained
326    GeneAnnot               Revised annotation of Affymetrix human gene probe sets    
350    GeneCards               Integrated database of human genes, maps, proteins and diseases
348    GeneLoc                 Gene location database                                    
 59    GenMapDB                Mapped human BAC clones                                   
324    HOWDY                   Human organized whole genome database                     
 77    Human BAC Ends DB       Non-redundant human BAC end sequences                     
597    Human Genome Seg-       Segmental duplications in the human genome                
       mental Duplication DB
61     IXDB                    Physical maps of human chromosome X                       
 54    Map Viewer            Display of genomic information by chromosomal position  
859    QTL Matchmaker        Quantitative trait loci mapping in human, mouse and rat 
 62    RHdb                  Radiation hybrid map data                               
592    SKY/M-FISH and CGH    Fluorescent images of chromosomes and cytogenetic data  
596    The Chromosome 7      Human chromosome 7 sequence and annotation              
       Annotation Project
684    TRBase                Tandem repeats in the human genome                      
316    UCSC Genome           Genome assemblies and annotation                        
319    UniSTS                Unified view of sequence tagged sites with mapping data 
1149   X:MAP                 Annotation and visualization of genome structure for Affymetrix
                             exon array analysis
       7.3. Human proteins
 911   Consensus CDS         Collaborative effort to identify a core set of human proteins
1072   Evola                 Human genes and their vertebrate orthologs              
 465   FANTOM                Functional annotation of mouse full-length cDNA clones  
  37   FLJ-DB                Annotated full-length human cDNAs (formerly HUNT database)
1037   GeneSpeed             Protein domains in the expressed human, mouse, fly and worm
685    H-InvDB               Full-length human cDNA clones                           
687    Hoppsigen             Human and mouse homologous processed pseudogenes        
500    HPRD                  Human protein reference database: domain architecture, post-
                             translational modifications, and disease association
171    HUGE                  Human unidentified gene-encoded large (>50 kDa) protein and
                             cDNA sequences
696    IPI                   International Protein Index                             
522    LIFEdb                Localization, interaction and functions of human proteins
600    Mammalian Gene        Full-length open reading frame clones for human, mouse, and rat
       Collection            genes
 545   NetAffx               Public Affymetrix probesets and annotations             
 550   ORFDB                 Collection of ORFs that are sold by Invitrogen          
1028   PlasmID               A repository for collection and distribution of plasmid clones
  4    STACK                 Sequence tag alignment and consensus knowledgebase      
 220   SYSTERS               Systematic re-searching and clustering of proteins      
 312   trome, trEST, trGEN   Databases of predicted human protein sequences          
  6    UniGene               Unified clusters of ESTs and full-length mRNA sequences 
       8. Human Genes and Diseases

       8.1. General human genetics databases
661    DG-CST                Disease gene conserved sequence tags                        
 57    GenAtlas              Human genes, markers and phenotypes                         
479    Genetics Home         A general guide on human hereditary diseases                
680    HAGR                  Human ageing genomic resources: Genes related to ageing in  
                             humans and model organisms
683    HCAD                  Human chromosome aberration database: Chromosomal           
                             breakpoints and affected genes
 133   HGMD                  Human gene mutation database                                          Requires user registration
1087   Human PAML Browser    Positive selection in human genes detected through genome   
1100   MSY Breakpoint        Sequence-tagged sites in the human Y chromosome             
1102   MutDB                 Predicted biochemical effects of human genetic variation: maping of
                             SNPs on protein sequence and structure
143    OMIM                  Online Mendelian inheritance in man: A catalog of human genetic
                             and genomic disorders                                                 IM
1163   SNP2NMD               Human SNPs causing nonsense-mediated mRNA decay             
       8.2. General polymorphism databases
119    ALFRED                Allele frequencies and DNA polymorphisms                    
793    CTGA                  Database for genetic disorders in Arabs                     
654    Cypriot national      Disease mutations in the Cypriot population                 
       mutation database
125    Cytokine Gene Poly-   Cytokine gene polymorphism literature database              
       morphism Database
655    Database of Genomic   Human genomic variants: frequency, segmental duplications and
       Variants              genome assembly gaps
595    dbQSNP                Quantification of SNP allele frequencies database           
886    dbRIP                 Human retrotransposon insertion polymorphism                
127    dbSNP                 Database of single nucleotide polymorphisms                 
966    D-HaploDB             Definitive haplotype database                               
669    FESD                  Functional Element SNPs Database: SNPs located within       
                             promoters, UTRs, etc., of human genes
1020   FINDBase              Frequencies of INherited Disorders                          
1074   F-SNP                   Functional effects of various human SNPs                   
 344   HapMap Project          A haplotype map of the human genome with patterns of DNA   
                               sequence variation
131    HGVbase                 Human genome variation database: Curated human             
496    HGVS Databases          A compilation of human mutation databases                  
517    JSNP                    Japanese SNP database                                      
665    PhenomicDB              Comparison of phenotypes of orthologous genes in human and 
                               model organisms
 973   PolyDoms                Human coding SNPs mapped onto protein domains              
 724   Polymorphix             Database of sequence polymorphisms                         
 146   Protein Mutant DB       Compilation of protein mutant data                         
1011   SNAP                    An integrated SNP Annotation Platform                      
1030   SNP@Ethnos              Human SNPs and genes that contain human ethnic variation   
 626   SNPeffect & PupaSuite   Phenotypic effects of human coding SNPs                    
 590   TopoSNP                 Topographic database of non-synonymous SNPs                
 755   TPMD                    Taiwan polymorphic microsatellite marker database          
       8.3. Cancer gene databases
122    Atlas of Genetics and   Cancer related genes, chromosomal abnormalities in oncology and
       Cytogenetics in Onco-   haematology, and cancer-prone diseases
       logy and Haematology
593    Cancer Chromosomes      Cytogenetic, clinical, and reference information on cancer-related
                               aberrations                                                          ncerchromosomes
 951   CancerGenes             Gene selection resource for cancer genome projects         
1053   CanGEM                  Gene copy number changes in cancer                         
 431   CGED                    Cancer Gene Expression Database                            
 651   COSMIC                  Catalogue Of Somatic Mutations In Cancer: Sequence data,   
                               samples and publications
126    Database of Germline    Mutations in human tumor and cell line p53 gene            
       p53 Mutations                                                                                m
889    EHCO                    Encyclopedia of hepatocellular carcinoma genes online      
822    HPTAA                   Human potential tumor-associated antigens                  
134    Human p53, human        Mutations at the human p53 and hprt genes; rodent transgenic lacI
       hprt, rodent lacI and   and lacZ mutations
       rodent lacZ databases
 362   IARC TP53 Database      Human TP53 somatic and germline mutations                  
 833   ITTACA                  Integrated tumor transcriptome array and clinical data analysis
1096   MethyCancer             Links between DNA methylation levels and cancer            
1026   OncoDB.HCC              Oncogenomic database of hepatocellular carcinoma           
 153   Oral Cancer Gene DB    Cellular and molecular data for genes involved in oral cancer     Incorporated into TGDBs, no. 155
1125   PubMeth                Links between DNA methylation levels and cancer         
 579   SNP500Cancer           Re-sequenced SNPs from 102 reference samples            
 149   SV40 Large T-Antigen   Mutations in SV40 large tumor antigen gene              
       Mutant Database
922    Tumor Associated       Tumor-associated genes database                         
       Gene Database
155    Tumor Gene Family      Cellular, molecular and biological data about genes involved in
       Databases (TGDBs)      various cancers
768    ALPSbase               Autoimmune lymphoproliferative syndrome database        
       8.4. Gene-, system- or disease-specific databases
788    AlzGene                Candidate genes for Alzheimer disease                   
120    Androgen Receptor      Mutations in the androgen receptor gene                 
       Gene Mutations DB
393    AngioDB                Database of angiogenesis and angiogenesis-related molecules
416    BayGenomics            Publicly available mouse gene trap cell lines                     Superseded by Gene Trap database, no. 827
417    BGED                   Brain Gene Expression Database                          
123    BTKbase                Mutation registry for X-linked agammaglobulinemia       
594    CarpeDB                Comprehensive database on the genetics of epilepsy      
124    CASRDB                 Calcium-sensing receptor database: CASR mutations causing
                              hypercalcemia and/or hyperparathyroidism
137    Collagen Mutation DB   Human type I and type III collagen gene mutations       
887    DENIZ                  Beta-thalassemia allele frequencies in world populations          No longer maintained
454    EICO DB                Expression-based Imprint Candidate Organiser            
110    EpoDB                  Genes expressed during human Erythropoiesis database    
460    ERGDB                  Estrogen Responsive Genes Database                      
464    EyeSite                Families of proteins functioning in the eye             
363    GOLD.db                Genomics Of Lipid-associated Disorders                  
130    HaemB                  Factor IX gene mutations, insertions and deletions      
491    HbVar                  Human hemoglobin variants and thalassemias              
907    HDBase                 A website for Huntington's disease research             
493    HemBase                Genes expressed in differentiating human erythroid cells
494    HemoPDB                Hematopoietic Promoter Database                         
366    HORDE                  Human Olfactory Receptor Data Exploratorium             
293    HOX-PRO                Homeobox genes database                                 
499    HPMR                   Human plasma membrane receptome: sequences, literature, and
                              expression data
135    Human PAX2 Allelic       Mutations in human PAX2 gene                              
       Variant Database
136    Human PAX6 Allelic       Mutations in human PAX6 gene                              
       Variant Database
501    IL2Rgbase                X-linked severe combined immunodeficiency mutation database
294    Imprinted Gene           Imprinted genes and parent-of-origin effects in animals   
506    INFEVERS                 Hereditary inflammatory disorder and familial mediterranean fever
                                mutation data
949    KBERG                    KnowledgeBase for Estrogen Responsive Genes               
139    KinMutBase               Disease-causing protein kinase mutations                  
523    Lowe Syndrome            Mutations causing Lowe oculocerebrorenal syndrome         
       Mutation Database
 142   NCL Resource             Polymorphisms in neuronal ceroid lipofuscinoses genes     
1025   NEIbank                  EyeSAGE, EyeBrowse and Eye Disease Gene databases         
 144   PAHdb                    Mutations at the phenylalanine hydroxylase locus          
 559   PGDB                     Prostate and prostatic diseases gene database             
 145   PHEXdb                   PHEX mutations causing X-linked hypophosphatemia          
 154   Prostate Expression DB   Prostate expression database: ESTs from prostate tissue and cell
                                type-specific cDNA libraries
147    PTCH1 Mutation DB        Mutations and SNPs found in PTCH1 gene                    
148    RB1 Gene Mutation DB     Mutations in the human retinoblastoma (RB1) gene          
769    SCAdb                    Spinocerebellar ataxia candidate gene database            
787    SynDB                    Synapse protein database                                  
632    T1Dbase                  A resource for type 1 diabetes research                   
752    The Autism Chromoso-     Curated collection of genomic features related to autism  
       me Rearrangement DB
753    The Lafora Database      The Lafora progressive myoclonus epilepsy mutation and    
                                polymorphism database
907    T-REGs                   A list of TGFbeta-responsive genes                                  No longer maintained

       9. Microarray Data and other Gene Expression Databases
1043   4DXpress                 Database for cross species expression pattern comparisons 
 634   5'SAGE                   5'-end serial analysis of gene expression                 
 338   ArrayExpress             Public collection of microarray gene expression data      
  11   Axeldb                   Gene expression in Xenopus laevis                         
 802   CAGE                     CAGE tags for cap-analysis of gene expression             
 427   CATMA                    Complete Arabidopsis Transcriptome MicroArray             
 432   CleanEx                  Expression reference database, linking heterogeneous expression
                                 data to facilitate cross-dataset comparisons
1064   CycleBase                 Gene expression profiles from cell-cycle microarray studies
 657   dbERGEII                  Database of experimental results on gene expression: Genomic
                                 alignment, annotation and experimental data
1170   dbLEP                     Database of Liver proteome expression profiles            
 812   EMAGE                     Edinburgh mouse atlas gene expression database            
  13   EPConDB                   Gene expression in pancreatic development, beta cell function and
987    Gene Aging Nexus          Aging-related gene expression data                        
 24    Gene Expression in        Gene expression in dental tissue                          
       Tooth Database
325    GeneNote                  Human genes expression profiles in healthy tissues        
330    GenePaint                 Gene expression patterns in the mouse                     
676    GeneTide                  A transcriptome-focused member of the GeneCards suite     
481    GeneTrap                  Expression patterns in an embryonic stem library of gene trap
918    GENSAT                    Gene Expression Nervous System Atlas: a map of gene expression
                                 in the central nervous system of the mouse                          nsat
603    GEO                       Gene Expression Omnibus: Public gene expression repository
485    GermOnline                Gene expression in mitotic and meiotic cell cycle         
891    GPX-Macrophage            Gene expression in macrophages                            
 23    HuGEIndex                 Human Gene Expression Index: Expression levels in normal  
16     Interferon Stimulated     Genes induced by treatment with interferons               
       Gene Database
827    International Gene Trap   Publicly available gene trap cell lines in mouse          
       Consortium DB
17     Kidney Development        Kidney development and gene expression                    
778    LOLA                      List of lists annotated: a comparison of gene sets identified in
                                 different microarray experiments
1092   M3D                       Many Microbe Microarrays Database                         
  18   MAGEST                    Ascidian (Halocynthia roretzi) gene expression patterns   
 699   MAMEP                     Molecular Anatomy of the Mouse Embryo Project             
 339   MEPD                      Gene expression in medaka (freshwater fish Oryzias latipes)
 541   NASCarrays                Nottingham Arabidopsis Stock Centre microarray database   
 709   OncoMine                  Cancer microarray data by gene or cancer type             
 558   PEPR                      Public Expression Profiling Resource                      
 568   RefExA                    Reference database for human gene expression analysis     
 739   rOGED                     Rat ovarian gene expression database                      
 712   SAGEmap                    NCBI's resource for SAGE data from various organisms        
 742   SIEGE                      Smoking Induced Epithelial Gene Expression                  
  22   Stanford Microarray DB     Raw and normalized data from microarray experiments         
1139   TMAD                       The Stanford Tissue Microarray Database                     
 905   TmaDB                      Tissue microarray database                                  

       10. Proteomics Resources
 606   2D-PAGE                    Proteome database system for microbial research             
1050   Biodefense Proteomics      Proteomics and host-pathogen interactions for biodefense-related
       Resource Center            microorganisms
731    DynaProt 2D                Proteome database of Lactococcus lactis                     
222    GELBANK                    2D gel electrophoresis patterns of proteins from complete microbial
950    MAPU                       Max-Planck Unified proteome database                        
710    Open Proteomics DB         Mass-spectrometry-based proteomics data for human, yeast, E. coli
                                  and Mycobacterium
850    PepSeeker                  Peptide identification and ion information from proteome    
                                  experiments                                                           bin/pepseeker/
851    PeptideAtlas               Peptides identified in LC-MS/MS proteomics experiments      
721    PlantMarkers               Database of predicted molecular markers from plants         
857    PRIDE                      Proteomics peptide identification database                  
225    SWISS-2DPAGE               Annotated 2D gel electrophoresis database                   

       11. Other Molecular Biology Databases
 256   BioImage                   Database of multidimensional biological images              
 801   BioModels                  Published mathematical models of biological interest        
1171   Déjà vu                    Duplicate citations in the scientific literature            
 298   PubMed                     Citations and abstracts of biomedical literature            
 992   University of Pittsburgh   A collection of bioinformatic databases and software tools  
       Resources Collection
701    MetaRouter                 Compounds and pathways related to bioremediation            
       11.1. Drugs and drug design
407    ANTIMIC                    Database of natural antimicrobial peptides                            http://research.i2r.a-
 408   APD                        Antimicrobial Peptide Database                              
1055   CEBS                       Database of toxicogenomics, microarray and proteomics data. 
 443   DART                    Drug Adverse Reaction Targets                                
 811   DrugBank                Combined information on drugs and drug targets               
 819   GLIDA                   G-protein coupled receptors ligand database                  
1002   PharmGED                PharmacoGenetic Effect Database                              
 392   PharmGKB                Pharmacogenomics and Pharmacogenetics Knowledge Base         
 741   Scorpion                Database of scorpion toxins                                  
 902   SuperDrug               2D and 3D chemical structures of various drugs               
 903   SuperNatural            Natural compounds and their suppliers                        
1136   SuperTarget             Drug-related information: medical indications, adverse drug effects,
                               drug metabolism and Gene Ontology terms of the target proteins
 315   TTD                     Therapeutic target database                                  
1147   VIOLIN                  Vaccine Investigation and Online Information Network         
       11.2. Molecular probes and primers
781    AOBase                  Antisense oligonucleotide selection and design               
505    IMGT/PRIMER-DB          Immunogenetics oligonucleotide primer database               
296    MPDB                    Molecular Probe Database                                     
728    Primer Studio           PCR primers for eukaryotic and prokaryotic genes             
390    probeBase               rRNA-targeted oligonucleotide probe sequences, DNA microarray
                               layouts, and associated information
 736   QPPD                    Quantitative PCR Primer Database                             
1008   qPrimerDepot            Quantitative real time PCR primers for human RefSeq sequences
 356   RTPrimerDB              Real-time PCR primer and probe sequences                     
 303   VirOligo                Virus-specific oligonucleotides for PCR and hybridization    

       12. Organelle Databases
804    Chloroplast genome DB   Chloroplast genome database                                  
 74    GOBASE                  Organelle genome database                                    
713    Organelle DB            Organelle proteins and subcellular structures                
601    Organelle genomes       NCBI's organelle genome resource                             
1001   PeroxisomeDB            Peroxisomal proteins, metabolic routes and diagnostic tools  
1115   Plant Organelles DB     Images and protocols for plant organelle research            
 722   PLprot                  Plastid protein database                                     
       12.1. Mitochondrial Genes and Proteins
637    AMPDB                   Arabidopsis Mitochondrial Protein Database                   
 686   HMPD                     Human mitochondrial protein database                         
1174   HmtDB                    Human mitochondrial database                                 
 824   Human MtDB               Human mitochondrial genome database                          
  38   HvrBase++                Primate mitochondrial DNA control region sequences           
 894   MamMiBase                Mammalian mitochondrial genome database                      
  64   Mitochondriome           Metazoan mitochondrial genes                                 
  83   MitoDat                  Mitochondrial proteins (predominantly human)                 
  84   MITOMAP                  Human mitochondrial genome                                   
1099   Mitome                   Comparative analysis of metazoan mitochondrial genomes       
  86   MITOP2                   Mitochondrial proteins, genes and diseases                   
 532   MitoProteome             Experimentally described human mitochondrial proteins        
 538   MPIMP db                 Mitochondrial protein import machinery of plants and yeast   
547    OGRe                     Organellar Genome Resource                                   

       13. Plant Databases

       13.1. General plant databases
599    BarleyBase               Expression profiling of plant genomes                        
982    Cereal Small RNA DB      Small RNAs expressed in rice and maize                       
624    CR-EST                   Cropp ESTs: Barley, wheat, pea, and potato ESTs              
888    DRASTIC                  Database resource for analysis of signal transduction in plant cells
128    FLAGdb++                 Integrative database about plant genomes                     
 672   GabiPD                   Central database of the German Plant Genome Project          
 675   GeneFarm                 Expert annotation of Arabidopsis gene and protein families   
 351   GénoPlante-Info          Plant genomic data from the Génoplante consortium            
 488   GrainGenes               Genes and phenotypes of wheat, barley, rye, triticale, oats  
 607   Gramene                  A resource for comparative grass genomics                    
1095   MetaCrop                 Biochemical pathways and enzymes in crop plants              
1029   MIPSPlantsDB             MIPS Plants Databases                                        
 581   openSputnik              Plant EST clustering and functional annotation                         No longer maintained
 999   PathoPlant               Signal transduction related to plant-pathogen interactions   
 853   Phytome                  Comparative genomics of plant species                        
 956   Plant DNA C-values       Genome sizes of various plants and algae                     
562    Plant Genome Central     NCBI’s portal for various large-scale plant genome and EST   
                                sequencing projects                                                    List.html
 843   Plant MPSS               Massively parallel signature sequencing of plant genes       
1116   Plant Stress-Responsi-   Stress-responsive gene in various plant species              
       ve Gene Catalog
 355   PlantGDB                Plant genome database: Actively-transcribed plant genes    
1118   PlantTribes             Families of protein-coding genes from five sequenced plant species
 948   POGs/PlantRBP           Orthologous groups of RNA binding proteins in plants       
1119   PPDB                    Plant promoter database                                    
 578   SeedGenes               Genes essential for Arabidopsis development                
 940   TIGR Plant Transcript   Transcript assemblies of plant EST and cDNA sequences      
       Assembly database
313    TropGENE DB             Genes and genomes of sugarcane, banana, cocoa              
 67    UK CropNet              Genome mapping in crop plants                              
       13.2. Arabidopsis thaliana
636    AGNS                    Arabidopsis GeneNet supplementary                          
618    AGRIS                   Arabidopsis gene regulatory information server             
780    Arabidopsis MPSS        Arabidopsis gene expression detected by massively parallel 
                               signature sequencing
638    Arabidopsis Nucleolar   Comparative analysis of human and Arabidopsis nucleolar    
       Protein Database        proteomes                                                            bin/atnopdb/proteome_comparison
640    Arabidopsis Small RNA   Arabidopsis Small RNA sequences                            
880    ARTADEdb                Arabidopsis tiling-array-based detection of exons          
394    AtGDB                   Arabidopsis thaliana genome database                       
765    AthaMap                 Genome-wide map of putative transcription factor binding sites in
                               Arabidopsis thaliana
934    ATTED-II                Coexpressed gene sets and gene regulators in Arabidopsis   
610    Brassica BASC           Database for Brassica genomic research                     
1054   CATdb                   Arabidopsis transcriptome data                             
 656   DATF                    Database of Arabidopsis transcription factors              
 935   GABI-Kat                Flanking sequence tags for T-DNA insertions in Arabidopsis 
1081   GreenPhylDB             Comparative genomics of rice and Arabidopsis thaliana      
 527   MAtDB                   MIPS Arabidopsis thaliana database                         
1004   PlantQTL-GE             Quantitative trait locus analysis in Arabidopsis and rice  
 738   RARGE                   RIKEN Arabidopsis genome encyclopedia: cDNAs, mutants and  
                               microarray data
 97    TAIR                    The Arabidopsis information resource                       
627    WAtDB                   Wageningen Arabidopsis thaliana Database                             No longer maintained
       13.3. Rice
418    BGI-RISe                Beijing Genomics Institute Rice Information System         
1156   DRTF                   Database of Rice Transcription Factors                   
  79   INE                    Integrated rice genome explorer                          
 353   IRIS -                 International Rice Information System                    
 536   MOsDB                  MIPS Oryza sativa database                               
 848   OryGenesDB             Rice genes, T-DNA and Ds flanking sequence tags          
 628   Oryza Tag Line         T-DNA insertion mutants of rice                          
  90   Oryzabase              Rice genetics and genomics                               
 860   RAP-DB                 Rice annotation project database                         
 737   Rice Annotation DB     Contig data for manual annotation of rice genome         
 861   Rice Mutant Database   Rice mutant database                                     
 569   Rice Pipeline          Unification tool for rice databases                      
 572   Rice Proteome DB       Rice proteome database                                   
 336   RiceGAAS               Rice genome automated annotation system                  
       13.4. Other plants
 971   ForestTreeDB           Annotated ESTs from diverse organs of conifer and poplar trees
1078   Genome Database for    Genetics and genomics data on apple, cherry, peach, pear,
       Rosaceae               raspberry, rose and strawberry
80     Legume Information     Legume information server (formerly Medicago genome initiative):
       System                 ESTs, gene expression and proteomic data
 526   MaizeGDB               Maize genetics and genomics database                     
1159   MedicCyc               Biochemical pathways in Medicago truncatula              
 539   MtDB                   <I>Medicago trunculata</I> Database                      
 921   NRESTdb                Natural Rubber EST Database                              
 849   Panzea                 Maize genome project data                                
 620   PoMaMo                 Potato Maps and More                                     
 766   SGMD                   Soybean genomics and microarray database                 
1132   Shanghai Rapeseed      Seed development and fatty acid metabolism of oilseed crops
 919   SoyBase                Genetic, genomic and phenotypic information about soybean
 870   SoyGD                  Soybean genome database                                  
 872   TED                    Tomato expression database                               
 874   TIGR Maize database    Maize genome sequencing consortium site                  
1016   TomatEST DB            EST collection from multiple tomato species              
          14. Immunological Databases
    799   AntiJen                  Quantitative binding data for peptides and proteins of       
                                   immunological interest
    642   BCIpep                   Database of B-cell epitopes                                  
    604   dbMHC                    Genetic and clinical database of the human MHC               
    813   Epitome                  Antigenic epitopes in proteins and antibodies that bind them 
    150   FIMM                     Functional molecular immunology data                         
    682   Haptendb                 Curated database of hapten molecules                         
    172   IMGT                     International immunogenetics information system:             
                                   Immunoglobulins, T cell receptors, MHC, and RPI
    503   IMGT/GENE-DB             Vertebrate immunoglobulin and T cell receptor genes          
    173   IMGT/HLA                 Polymorphism of human MHC and related genes                  
    504   IMGT/LIGM-DB             Immunoglobulin, T cell receptor and MHC nucleotide sequences 
                                   from human and other vertebrates
    779   Immune epitope DB        Antibody and T cell epitopes for primates, rodents, and other
    367   IPD                      Immuno Polymorphism Database                                 
    692   IPD-ESTDAB               Immunologically characterised melanoma cell lines            
    693   IPD-HPA                  Human platelet antigens                                      
    694   IPD-KIR                  Killer-cell Immunoglobulin-like Receptors                    
    691   IPD-MHC                  Sequences of the major histocompatibility complex            
    361   JenPep                   Quantitative binding data for peptides and proteins of                 Superseded by AntiJen, no. 799
                                   immunological interest
 702      MHCBN                    Database of MHC binding and non-binding peptides             
 181      MHCPEP                   MHC-binding peptides                                         
1101      MUGEN Mouse DB           Murine models of immune processes and immunological diseases 
 967      SuperHapten              A comprehensive database for small immunogenic compounds     
 621      VBASE2                   Variable genes from the Ig loci of human and mouse           

 – Each database is shown in the list only once. In another version of this list, available at the NAR web site, a
database can be listed under two (sub)categories.
 – Accession number of the database in the on-line list; can be used to view the database summary. For example, shows the summary for DDBJ.
    – In some database names, the word "database" is abbreviated as “DB”.

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