Nucleotide Sequence Databases
1.1 International Nucleotide Sequence Database Collaboration

Database name	Full name and/or description	URL
DDBJ-DNA Data Bank of Japan	All known nucleotide and protein sequences	http://www.ddbj.nig.ac.jp
EMBL-Nucleotide Sequence Database	All known nucleotide and protein sequences	http://www.ebi.ac.uk/embl.html
GenBank	All known nucleotide and protein sequences	http://www.ncbi.nlm.nih.gov/Entrez

1.2. DNA sequences: genes, motifs and regulatory sites
1.2.1. Coding and coding DNA

Database name	Full name and/or description	URL
ACLAME	A classification of genetic mobile elements	http://aclame.ulb.ac.be/
CUTG	Codon usage tabulated from GenBank	http://www.kazusa.or.jp/codon/
Genetic Codes	Genetic codes in various organisms and organelles	http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
Entrez Gene	Gene-centered information at NCBI	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene
HERVd	Human endogenous retrovirus database	http://herv.img.cas.cz
Hoppsigen	Human and mouse homologous processed pseudogenes	http://pbil.univ-lyon1.fr/databases/hoppsigen.html
Imprinted Gene Catalogue	Imprinted genes and parent-of-origin effects in animals	http://www.otago.ac.nz/IGC
Islander	Pathogenicity islands and prophages in bacterial genomes	http://www.indiana.edu/~islander
MICdb	Prokaryotic microsatellites	http://www.cdfd.org.in/micas
NPRD	Nucleosome positioning region database	http://srs6.bionet.nsc.ru/srs6/
STRBase	Short tandem DNA repeats database	http://www.cstl.nist.gov/div831/strbase/
TIGR Gene Indices	Organism-specific databases of EST and gene sequences	http://www.tigr.org/tdb/tgi.shtml
Transterm	Codon usage, start and stop signals	http://uther.otago.ac.nz/Transterm.html
UniGene	Non-redundant set of eukaryotic gene-oriented clusters	http://www.ncbi.nlm.nih.gov/UniGene/
UniVec	Vector sequences, adapters, linkers and primers used in DNA cloning, can be used to check for vector contamination	http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html
VectorDB	Characterization and classification of nucleic acid vectors	http://genome-www2.stanford.edu/vectordb/
Xpro	Eukaryotic protein-encoding DNA sequences, both intron-containing and intron- less genes	http://origin.bic.nus.edu.sg/xpro/

1.2.2. Gene structure, introns and exons, splice sites

Database name	Full name and/or description	URL
ASAP	Alternative spliced isoforms	http://www.bioinformatics.ucla.edu/ASAP
ASD	Alternative splicing database at EBI, includes three databases AltSplice, AltExtron and AEdb	http://www.ebi.ac.uk/asd
ASDB	Alternative splicing database: protein products and expression patterns of alternatively spliced genes	http://hazelton.lbl.gov/~teplitski/alt
ASHESdb	Alternatively spliced human genes by exon skipping database	http://sege.ntu.edu.sg/wester/ashes/
EASED	Extended alternatively spliced EST database	http://eased.bioinf.mdc-berlin.de/
ECgene	Genome annotation for alternative splicing	http://genome.ewha.ac.kr/ECgene/
EDAS	EST-derived alternative splicing database	http://www.ig-msk.ru:8005/EDAS/
ExInt	Exon�intron structure of eukaryotic genes	http://sege.ntu.edu.sg/wester/exint/
HS3D	Homo sapiens splice sites dataset	http://www.sci.unisannio.it/docenti/rampone/
Intronerator	Alternative splicing in C.elegans and C.briggsae	http://www.cse.ucsc.edu/~kent/intronerator/
Spliced	Canonical and non-canonical mammalian splice sites	http://www.softberry.com/berry.phtml?topic= splicedb&group=data&subgroup=spldb
SpliceInfo	Modes of alternative splicing in human genome	http://140.115.50.96/SpliceInfo/
SpliceNest	A tool for visualizing splicing of genes from EST data	http://splicenest.molgen.mpg.de/

1.2.3. Transcriptional regulator sites and transcription factors

Database name	Full name and/or description	URL
ACTIVITY	Functional DNA/RNA site activity	http://wwwmgs.bionet.nsc.ru/mgs/systems/activity/
DBTBS	Bacillus subtilis promoters and transcription factors	http://dbtbs.hgc.jp/
DoOP	Database of orthologous promoters: chordates and plants	http://doop.abc.hu/
DPInteract	Binding sites for E.coli DNA-binding proteins	http://arep.med.harvard.edu/dpinteract
EPD	Eukaryotic promoter database	http://www.epd.isb-sib.ch
HemoPDB	Hematopoietic promoter database: transcriptional regulation in hematopoiesis	http://bioinformatics.med.ohio-state.edu/HemoPDB
JASPAR	PSSMs for transcription factor DNA-binding sites	http://jaspar.cgb.ki.se
MAPPER	Putative transcription factor binding sites in various genomes	http://bio.chip.org/mapper
PLACE	Plant cis-acting regulatory DNA elements	http://www.dna.affrc.go.jp/htdocs/PLACE
PlantCARE	Plant promoters and cis -acting regulatory elements	http://intra.psb.ugent.be:8080/PlantCARE/
PlantProm	Plant promoter sequences for RNA polymerase II	http://mendel.cs.rhul.ac.uk/
PRODORIC	Prokaryotic database of gene regulation networks	http://prodoric.tu-bs.de/
PromEC	E . coli promoters with experimentally identified transcriptional start sites	http://bioinfo.md.huji.ac.il/marg/promec
SELEX_DB	DNA and RNA binding sites for various proteins, found by systematic evolution of ligands by exponential enrichment	http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/
TESS	Transcription element search system	http://www.cbil.upenn.edu/tess
TRACTOR db	Transcription factors in gamma-proteobacteria database	http://www.tractor.lncc.br/
TRANSCompel	Composite regulatory elements affecting gene transcription in eukaryotes	http://www.gene-regulation.com/pub/databases.html#transcompel
TRANSFAC	Transcription factors and binding sites	http://transfac.gbf.de/TRANSFAC/index.html
TRED	Transcriptional regulatory element database	http://rulai.cshl.edu/tred
TRRD	Transcription regulatory regions of eukaryotic genes	http://www.bionet.nsc.ru/trrd/

2. RNA sequence databases

Database name	Full name and/or description	URL
16S and 23S rRNA Mutation Database	16S and 23S ribosomal RNA mutations	http://www.fandm.edu/Departments /Biology/Databases/RNA.html
5S rRNA Database	5S rRNA sequences	http://biobases.ibch.poznan.pl/5SData/
Aptamer database	Small RNA/DNA molecules binding nucleic acids, proteins	http://aptamer.icmb.utexas.edu/
ARED	AU-rich element-containing mRNA database	http://rc.kfshrc.edu.sa/ared
Mobile group II introns	A database of group II introns, self-splicing catalytic RNAs	http://www.fp.ucalgary.ca/group2introns/
European rRNA database	All complete or nearly complete rRNA sequences	http://www.psb.ugent.be/rRNA/
GtRDB	Genomic tRNA database	http://rna.wustl.edu/GtRDB
Guide RNA Database	RNA editing in various kinetoplastid species	http://biosun.bio.tu-darmstadt.de/goringer/gRNA/gRNA.html
HIV Sequence Database	HIV RNA sequences	http://hiv-web.lanl.gov/
HuSiDa	Human siRNA database	http://itb1.biologie.hu-berlin.de/~nebulus/sirna/
HyPaLib	Hybrid pattern library : structural elements in classes of RNA	http://bibiserv.techfak.uni-bielefeld.de/HyPa/
IRESdb	Internal ribosome entry site database	http://ifr31w3.toulouse.inserm.fr/IRESdatabase/
microRNA Registry	Database of microRNAs (small non-coding RNAs)	http://www.sanger.ac.uk/Software/Rfam/mirna/
NCIR	Non-canonical interactions in RNA structures	http://prion.bchs.uh.edu/bp_type/
ncRNAs Database	Non-coding RNAs with regulatory functions	http://biobases.ibch.poznan.pl/ncRNA/
NONCODE	A database of non-coding RNAs	http://www.bioinfo.org.cn/NONCODE/index.htm
PLANTncRNAs	Plant non-coding RNAs	http://www.prl.msu.edu/PLANTncRNAs
Plant snoRNA DB	snoRNA genes in plant species	http://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home
PolyA_DB	A database of mammalian mRNA polyadenylation	http://polya.umdnj.edu/polyadb/
PseudoBase	Database of RNA pseudoknots	http://wwwbio.leidenuniv.nl/~Batenburg/PKB.html
Rfam	Non-coding RNA families	http://www.sanger.ac.uk/Software/Rfam/
RISSC	Ribosomal internal spacer sequence collection	http://ulises.umh.es/RISSC
RNAdb	Mammalian non-coding RNA database	http://ncrna.bioinformatics.com.au/
RNA Modification Database	Naturally modified nucleosides in RNA	http://medlib.med.utah.edu/RNAmods/
RRNDB	rRNA operon numbers in various prokaryotes	http://rrndb.cme.msu.edu/
siRNAdb	siRNA database and search engine	http://sirna.cgb.ki.se/
Small RNA Database	Small RNAs from prokaryotes and eukaryotes	http://mbcr.bcm.tmc.edu/smallRNA
SRPDB	Signal recognition particle database	http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html
SSU rRNA Modification Database	Modified nucleosides in small subunit rRNA	http://medstat.med.utah.edu/SSUmods/
Subviral RNA Database	Viroids and viroid-like RNAs	http://subviral.med.uottawa.ca/
tmRNA Website	tmRNA sequences and alignments	http://www.indiana.edu/~tmrna
tmRDB	tmRNA database	http://psyche.uthct.edu/dbs/tmRDB/tmRDB.html
tRNA sequences	tRNA viewer and sequence editor	http://www.uni-bayreuth.de/departments/biochemie/trna/
UTRdb/UTRsite	5' and 3' -UTRs of eukaryotic mRNAs	http://bighost.area.ba.cnr.it/srs6/

3. Protein sequence databases
3.1. General sequence databases

Database name	Full name and/or description	URL
EXProt	Sequences of proteins with experimentally verified function	http://www.cmbi.kun.nl/EXProt/
NCBI Protein database	All protein sequences: translated from GenBank and imported from other protein databases	http://www.ncbi.nlm.nih.gov/entrez /query.fcgi?db=Protein
PA-GOSUB	Protein sequences from model organisms, GO assignment and subcellular localization	http://www.cs.ualberta.ca/~bioinfo/ PA/ProteomeIndex.html
PIR-PSD	Protein information resource protein sequence database, has been merged into the UniProt knowledgebase	http://pir.georgetown.edu/
PIR-NREF	PIR's non-redundant reference protein database	http://pir.georgetown.edu/pirwww/pirnref.shtml
PRF	Protein research foundation database of peptides: sequences, literature and unnatural amino acids	http://www.prf.or.jp/en
Swiss-Prot	Now UniProt/Swiss-Prot: expertly curated protein sequence database, section of the UniProt knowledgebase	http://www.expasy.org/sprot
TrEMBL	Now UniProt/TrEMBL: computer-annotated translations of EMBL nucleotide sequence entries: section of the UniProt knowledgebase	http://www.expasy.org/sprot
UniParc	UniProt archive: a repository of all protein sequences, consisting only of unique identifiers and sequence	http://www.uniprot.org/database/archive.shtml
UniProt	Universal protein knowledgebase: merged data from Swiss-Prot, TrEMBL and PIR protein sequence databases	http://www.uniprot.org/
UniRef	UniProt non-redundant reference database: clustered sets of related sequences (including splice variants and isoforms)	http://www.uniprot.org/database/nref.shtml

3.2. Protein properties

Database name	Full name and/or description	URL
AAindex	Physicochemical properties of amino acids	http://www.genome.ad.jp/aaindex/
ProNIT	Thermodynamic data on protein�nucleic acid interactions	http://gibk26.bse.kyutech.ac.jp/jouhou/ pronit/pronit.html
ProTherm	Thermodynamic data for wild-type and mutant proteins	http://gibk26.bse.kyutech.ac.jp/jouhou/ protherm/protherm.html
TECRdb	Thermodynamics of enzyme-catalyzed reactions	http://xpdb.nist.gov/enzyme _thermodynamics/

3.3. Protein localization and targeting

Database name	Full name and/or description	URL
DBSubLoc	Database of protein subcellular localization	http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html
NESbase	Nuclear export signals database	http://www.cbs.dtu.dk/databases/NESbase
NLSdb	Nuclear localization signals	http://cubic.bioc.columbia.edu/db/NLSdb/
NMPdb	Nuclear matrix associated proteins database	http://www.rostlab.org/db/NMPdb/
NOPdb	Nucleolar proteome database	http://www.lamondlab.com/NOPdb/
PSORTdb	Protein subcellular localization in bacteria	http://db.psort.org/
SPD	Secreted protein database	http://spd.cbi.pku.edu.cn
THGS	Transmembrane helices in genome sequences	http://pranag.physics.iisc.ernet.in/thgs/
TMPDB	Experimentally characterized transmembrane topologies	http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/

3.4. Protein sequence motifs and active sites

Database name	Full name and/or description	URL
ASC	Active sequence collection: biologically active peptides	http://bioinformatica.isa.cnr.it/ASC/
Blocks	Alignments of conserved regions in protein families	http://blocks.fhcrc.org/
CSA	Catalytic site atlas : active sites and catalytic residues in enzymes of known 3D structure	http://www.ebi.ac.uk/thornton-srv/databases/CSA/
COMe	Co-ordination of metals etc.: classification of bioinorganic proteins ( metalloproteins and some other complex proteins)	http://www.ebi.ac.uk/come
CopS	Comprehensive peptide signature database	http://203.195.151.46/copsv2/index.html
eBLOCKS	Highly conserved protein sequence blocks	http://fold.stanford.edu/eblocks/acsearch.html
eMOTIF	Protein sequence motif determination and searches	http://motif.stanford.edu/emotif
Metalloprotein Site Database	Metal-binding sites in metalloproteins	http://metallo.scripps.edu/
O-GlycBase	O- and C-linked glycosylation sites in proteins	http://www.cbs.dtu.dk/databases/OGLYCBASE/
PDBSite	3D structure of protein functional sites	http://srs6.bionet.nsc.ru/srs6/
Phospho.ELM	S/T/Y protein phosphorylation sites (formerly PhosphoBase)	http://phospho.elm.eu.org/
PROMISE	Prosthetic centers and metal ions in protein active sites	http://metallo.scripps.edu/PROMISE
PROSITE	Biologically significant protein patterns and profiles	http://www.expasy.org/prosite
ProTeus	Signature sequences at the protein N- and C-termini	http://www.proteus.cs.huji.ac.il/

3.5. Protein domain databases; protein classification

Database name	Full name and/or description	URL
ADDA	A database of protein domain classification	http://ekhidna.biocenter.helsinki.fi:8080 /examples/servlets/adda/
CDD	Conserved domain database, includes protein domains fromPfam, SMART, COG and KOG databases	http://www.ncbi.nlm.nih.gov/ Structure/cdd/cdd.shtml
CluSTr	Clusters of Swiss-Prot + TrEMBL proteins	http://www.ebi.ac.uk/clustr
FunShift	Functional divergence between the subfamilies of a protein domain family	http://funshift.cgb.ki.se/
Hits	A database of protein domains and motifs	http://hits.isb-sib.ch/
InterPro	Integrated resource of protein families, domains and functional sites	http://www.ebi.ac.uk/interpro
iProClass	Integrated protein classification database	http://pir.georgetown.edu/iproclass/
PIRSF	Family/superfamily classification of whole proteins	http://pir.georgetown.edu/pirsf/
PRINTS	Hierarchical gene family fingerprints	http://www.bioinf.man.ac.uk/ dbbrowser/PRINTS/
Pfam	Protein families: multiple sequence alignments and profile hidden Markov models of protein domains	http://www.sanger.ac.uk/Software/Pfam/
PRECISE	Predicted and consensus interaction sites in enzymes	http://precise.bu.edu/precisedb/
ProDom	Protein domain families	http://www.toulouse.inra.fr/prodom.html
ProtoMap	Hierarchical classification of Swiss-Prot proteins	http://protomap.cornell.edu/
ProtoNet	Hierarchical clustering of Swiss-Prot proteins	http://www.protonet.cs.huji.ac.il/
S4	Structure-based sequence alignments of SCOP superfamilies	http://compbio.mds.qmw.ac.uk/~james/S4.shtml
SBASE	Protein domain sequences and tools	http://www.icgeb.org/sbase
SMART	Simple modular architecture research tool: signalling, extracellular and chromatin-associated protein domains	http://smart.embl-heidelberg.de/
SUPFAM	Grouping of sequence families into superfamilies	http://pauling.mbu.iisc.ernet.in/~supfam
SYSTERS	Systematic re-searching and clustering of proteins	http://systers.molgen.mpg.de/
TIGRFAMs	TIGR protein families adapted for functional annotation	http://www.tigr.org/TIGRFAMs

3.6. Databases of individual protein families

Database name	Full name and/or description	URL
AARSDB	Aminoacyl-tRNA synthetase database	http://rose.man.poznan.pl/aars/index.html
ASPD	Artificial selected proteins/peptides database	http://wwwmgs.bionet.nsc.ru/mgs/gnw/aspd/
BacTregulators	Transcriptional regulators of AraC and TetR families	http://www.bactregulators.org/
CSDBase	Cold shock domain-containing proteins	http://www.chemie.uni-marburg.de/~csdbase/
CuticleDB	Structural proteins of Arthropod cuticle	http://bioinformatics.biol.uoa.gr/cuticleDB
DCCP	Database of copper-chelating proteins	http://sdbi.sdut.edu.cn/DCCP/en/index.php
DExH/D Family Database	DEAD-box, DEAH-box and DExH-box proteins	http://www.helicase.net/dexhd/dbhome.htm
Endogenous GPCR List	G protein-coupled receptors; expression in cell lines	http://www.tumor-gene.org/GPCR/gpcr.html
ESTHER	Esterases and other alpha/beta hydrolase enzymes	http://www.ensam.inra.fr/esther
EyeSite	Families of proteins functioning in the eye	http://eyesite.cryst.bbk.ac.uk/
GPCRDB	G protein-coupled receptors database	http://www.gpcr.org/7tm/
gpDB	G-proteins and their interaction with GPCRs	http://bioinformatics.biol.uoa.gr/gpDB
Histone Database	Histone fold sequences and structures	http://research.nhgri.nih.gov/histones/
Homeobox Page	Homeobox proteins, classification and evolution	http://www.biosci.ki.se/groups/tbu/homeo.html
Hox-Pro	Homeobox genes database	http://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hox-pro00.html
Homeodomain Resource	Homeodomain sequences, structures and related genetic and genomic information	http://research.nhgri.nih.gov/homeodomain/
HORDE	Human olfactory receptor data exploratorium	http://bioinfo.weizmann.ac.il/HORDE/
InBase	Inteins (protein splicing elements) database: properties, sequences, bibliography	http://www.neb.com/neb/inteins.html
KinG�Kinases in Genomes	S/T/Y-specific protein kinases encoded in complete genomes	http://hodgkin.mbu.iisc.ernet.in/~king
Knottins	Database of knottins�small proteins with an unusual �disulfide through disulfide ' knot	http://knottin.cbs.cnrs.fr
LGICdb	Ligand-gated ion channel subunit sequences database	http://www.pasteur.fr/recherche/banques/LGIC/LGIC.html
Lipase Engineering Database Sequence	structure and function of lipases and esterases	http://www.led.uni-stuttgart.de/
LOX-DB	Mammalian, invertebrate, plant and fungal lipoxygenases	http://www.dkfz-heidelberg.de/spec/lox-db/
MEROPS	Database of proteolytic enzymes (peptidases)	http://merops.sanger.ac.uk/
NPD	Nuclear protein database	http://npd.hgu.mrc.ac.uk/
NucleaRDB	Nuclear receptor superfamily	http://www.receptors.org/NR/
Nuclear Receptor Resource	Nuclear receptor superfamily	http://nrr.georgetown.edu/NRR/nrrhome.htm
NUREBASE	Nuclear hormone receptors database	http://www.ens-lyon.fr/LBMC/laudet/nurebase.html
Olfactory Receptor Database	Sequences for olfactory receptor-like molecules	http://senselab.med.yale.edu/senselab/ordb/
ooTFD	Object-oriented transcription factors database	http://www.ifti.org/ootfd
PKR	Protein kinase resource: sequences, enzymology, genetics and molecular and structural properties	http://pkr.sdsc.edu/html/index.shtml
PLPMDB	Pyridoxal-5 0 -phosphate dependent enzymes mutations	http://www.studiofmp.com/plpmdb/
ProLysED	A database of bacterial protease systems	http://genome.ukm.my/prolyses/
Prolysis	Proteases and natural and synthetic protease inhibitors	http://delphi.phys.univ-tours.fr/Prolysis/
REBASE	Restriction enzymes and associated methylases	http://rebase.neb.com/rebase/rebase.html
Ribonuclease P Database	RNase P sequences, alignments and structures	http://www.mbio.ncsu.edu/RNaseP/home.html
RPG	Ribosomal protein gene database	http://ribosome.miyazaki-med.ac.jp/
RTKdb	Receptor tyrosine kinase sequences	http://pbil.univ-lyon1.fr/RTKdb/
S/MARt dB	Nuclear scaffold/matrix attached regions	http://smartdb.bioinf.med.uni-goettingen.de/
Scorpion	Database of scorpion toxins	http://research.i2r.a-star.edu.sg:8080/scorpion/
SDAP	Structural database of allergenic proteins and food allergens	http://fermi.utmb.edu/SDAP
SENTRA	Sensory signal transduction proteins	http://www-wit.mcs.anl.gov/sentra/
SEVENS	7-transmembrane helix receptors (G-protein-coupled)	http://sevens.cbrc.jp/
SRPDB	Proteins of the signal recognition particles	http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html
TrSDB	Transcription factor database	http://ibb.uab.es/trsdb
VKCDB	Voltage-gated potassium channel database	http://vkcdb.biology.ualberta.ca/
Wnt Database	Wnt proteins and phenotypes	http://www.stanford.edu/~rnusse/wntwindow.html

4. Structure Databases
4.1. Small molecules

Database name	Full name and/or description	URL
ChEBI	Chemical entities of biological interest	http://www.ebi.ac.uk/chebi/
CSD	Cambridge structural database: crystal structure information for organic and metal-organic compounds	http://www.ccdc.cam.ac.uk/prods/csd/csd.html
HIC-Up	Hetero-compound Information Centre� Uppsala	http://xray.bmc.uu.se/hicup
AANT	Amino acid�nucleotide interaction database	http://aant.icmb.utexas.edu/
Klotho	Collection and categorization of biological compounds	http://www.biocheminfo.org/klotho
LIGAND	Chemical compounds and reactions in biological pathways	http://www.genome.ad.jp/ligand/
PDB-Ligand	3D structures of small molecules bound to proteins and nucleic acids	http://www.idrtech.com/PDB-Ligand/
Ligand Depot	Ligand Depot is a data warehouse which integrates databases, services, tools and methods related to small molecules bound to macromolecules.	http://ligand-depot.rutgers.edu/
PubChem	Structures and biological activities of small organic molecules	http://pubchem.ncbi.nlm.nih.gov/

4.2. Carbohydrates

Database name	Full name and/or description	URL
CCSD	Complex carbohydrate structure database (CarbBank)	http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm
CSS	Carbohydrate structure suite: carbohydrate 3D structures derived from the PDB	http://www.dkfz.de/spec/css/
Glycan	Carbohydrate database, part of the KEGG system	http://glycan.genome.ad.jp/
GlycoSuiteDB	N- and O-linked glycan structures and biological sources	http://www.glycosuite.com/
Monosaccharide Browser	Space-filling Fischer projections of monosaccharides	http://www.jonmaber.demon.co.uk/monosaccharide
SWEET-DB	Annotated carbohydrate structure and substance information	http://www.dkfz-heidelberg.de/spec2/sweetdb/

4.3. Nucleic acid structure

Database name	Full name and/or description	URL
NDB	Nucleic acid-containing structures	http://ndbserver.rutgers.edu/
NTDB	Thermodynamic data for nucleic acids	http://ntdb.chem.cuhk.edu.hk/
RNABase	RNA-containing structures from PDB and NDB	http://www.rnabase.org/
SCOR	Structural classification of RNA: RNA motifs by structure, function and tertiary interactions	http://scor.lbl.gov/

4.4. Protein structure

Database name	Full name and/or description	URL
ArchDB	Automated classification of protein loop structures	http://gurion.imim.es/archdb
wwPDB	Worldwide Protein Data Bank	http://www.wwpdb.org/index.html
PDBj	Protein Data Bank Japan-the archive for macromolecular structures.	http://www.pdbj.org/
ASTRAL	Sequences of domains of known structure, selected subsets and sequence� structure correspondences	http://astral.stanford.edu/
BAliBASE	A database for comparison of multiple sequence alignments	http://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html
BioMagResBank	NMR spectroscopic data for proteins and nucleic acids	http://www.bmrb.wisc.edu/
CADB	Conformational angles in proteins database	http://cluster.physics.iisc.ernet.in/cadb/
CATH	Protein domain structures database	http://www.biochem.ucl.ac.uk/bsm/cath_new
CE 3D	protein structure alignments	http://cl.sdsc.edu/ce.html
CKAAPs DB	Structurally similar proteins with dissimilar sequences	http://ckaap.sdsc.edu/
Dali	Protein fold classification using the Dali search engine	http://www.bioinfo.biocenter.helsinki.fi:8080/dali/
Decoys �R' Us	Computer-generated protein conformations	http://dd.stanford.edu/
DisProt	Database of Protein Disorder: proteins that lack fixed 3D structure in their native states	http://divac.ist.temple.edu/disprot
DomIns	Domain insertions in known protein structures	http://stash.mrc-lmb.cam.ac.uk/DomIns
DSDBASE	Native and modeled disulfide bonds in proteins	http://www.ncbs.res.in/~faculty/mini/dsdbase/dsdbase.html
DSMM	Database of simulated molecular motions	http://projects.villa-bosch.de/dbase/dsmm/
eF-site	Electrostatic surface of Functional site: electrostatic potentials and hydrophobic properties of the active sites	http://ef-site.protein.osaka-u.ac.jp/eF-site
GenDiS	Genomic distribution of protein structural superfamilies	http://caps.ncbs.res.in/gendis/home.html
Gene3D	Precalculated structural assignments for whole genomes	http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/
GTD	Genomic threading database: structural annotations of complete proteomes	http://bioinf.cs.ucl.ac.uk/GTD
GTOP	Protein fold predictions from genome sequences	http://spock.genes.nig.ac.jp/~genome/
Het-PDB	Navi Hetero-atoms in protein structures	http://daisy.nagahama-i-bio.ac.jp/golab/hetpdbnavi.html
HOMSTRAD	Homologous structure alignment database: curated structure-based alignments for protein families	http://www-cryst.bioc.cam.ac.uk/homstrad
IMB Jena Image Library	Visualization and analysis of 3D biopolymer structures	http://www.imb-jena.de/IMAGE.html
IMGT/3Dstructure-DB	Sequences and 3D structures of vertebrate immunoglobulins, T cell receptors and MHC proteins	http://imgt3d.igh.cnrs.fr/
ISSD	Integrated sequence�structure database	http://www.protein.bio.msu.su/issd
LPFC	Library of protein family core structures	http://www-smi.stanford.edu/projects/helix/LPFC
MMDB	NCBI's database of 3D structures, part of NCBI Entrez	http://www.ncbi.nlm.nih.gov/Structure
E-MSD	EBI's macromolecular structure database	http://www.ebi.ac.uk/msd
ModBase	Annotated comparative protein structure models	http://alto.compbio.ucsf.edu/modbase-cgi/index.cgi
MolMovDB	Database of macromolecular movements: descriptions of protein and macromolecular motions, including movies	http://bioinfo.mbb.yale.edu/MolMovDB/
PALI	Phylogeny and alignment of homologous protein structures	http://pauling.mbu.iisc.ernet.in/~pali
PASS2	Structural motifs of protein superfamilies	http://ncbs.res.in/~faculty/mini/campass/pass.html
PepConfDB	A database of peptide conformations	http://www.peptidome.org/products/list.htm
PDB	Protein structure databank: all publicly available 3D structures of proteins and nucleic acids	http://www.rcsb.org/pdb
PDB-REPRDB	Representative protein chains, based on PDB entries	http://mbs.cbrc.jp/pdbreprdb-cgi/reprdb_menu.pl
PDBsum	Summaries and analyses of PDB structures	http://www.biochem.ucl.ac.uk/bsm/pdbsum
PDB_TM	Transmembrane proteins with known 3D structure	http://www.enzim.hu/PDB_TM/
Protein Folding Database	Experimental data on protein folding	http://pfd.med.monash.edu.au
SCOP	Structural classification of proteins	http://scop.mrc-lmb.cam.ac.uk/scop
Sloop	Classification of protein loops	http://www-cryst.bioc.cam.ac.uk/~sloop/
Structure Superposition Database	Pairwise superposition of TIM-barrel structures	http://ssd.rbvi.ucsf.edu/
SWISS-MODEL Repository	Database of annotated 3D protein structure models	http://swissmodel.expasy.org/repository
SUPERFAMILY	Assignments of proteins to structural superfamilies	http://supfam.org/
SURFACE	Surface residues and functions annotated, compared and evaluated: a database of protein surface patches	http://cbm.bio.uniroma2.it/surface
TargetDB	Target data from worldwide structural genomics projects	http://targetdb.pdb.org/
3D-GENOMICS	Structural annotations for complete proteomes	http://www.sbg.bio.ic.ac.uk/3dgenomics
TOPS	Topology of protein structures database	http://www.tops.leeds.ac.uk

5. Genomics Databases (non-human)
5.1. Genome annotation terms, ontologies and nomenclature

Database name	Full name and/or description	URL
Genew	Human gene nomenclature: approved gene symbols	http://www.gene.ucl.ac.uk/nomenclature
GO	Gene ontology consortium database	http://www.geneontology.org/
GOA	EBI's gene ontology annotation project	http://www.ebi.ac.uk/GOA
IUBMB Nomenclature database	Nomenclature of enzymes, membrane transporters, electron transport proteins and other proteins	http://www.chem.qmul.ac.uk/iubmb
IUPAC Nomenclature database	Nomenclature of biochemical and organic compounds approved by the IUBMB-IUPAC Joint Commission	http://www.chem.qmul.ac.uk/iupac
IUPHAR-RD	The International Union of Pharmacology recommendations on receptor nomenclature and drug classification	http://www.iuphar-db.org/iuphar-rd/
PANTHER	Gene products organized by biological function	http://panther.celera.com/
UMLS	Unified medical language system	http://umlsks.nlm.nih.gov/

5.1.1. Taxonomy and Identification

Database name	Full name and/or description	URL
ICB	gyrB database for identification and classification of bacteria	http://seasquirt.mbio.co.jp/icb/index.php
NCBI Taxonomy	Names of all organisms represented in GenBank	http://www.ncbi.nlm.nih.gov/Taxonomy/
PANDIT	Protein and associated nucleotide domains with inferred trees	http://www.ebi.ac.uk/goldman-srv/pandit/
RIDOM	rRNA-based differentiation of medical microorganisms	http://www.ridom-rdna.de/
RDP-II	Ribosomal database project	http://rdp.cme.msu.edu
Tree of Life	Information on phylogeny and biodiversity	http://phylogeny.arizona.edu/tree/phylogeny.html

5.2. General genomics databases

Database name	Full name and/or description	URL
COG	Clusters of orthologous groups of proteins	http://www.ncbi.nlm.nih.gov/COG
COGENT	Complete genome tracking: predicted peptides from fully sequenced genomes	http://maine.ebi.ac.uk:8000/services/cogent/
CORG	Comparative regulatory genomics: conserved non-coding sequence blocks	http://corg.molgen.mpg.de/
DEG	Database of essential genes from bacteria and yeast	http://tubic.tju.edu.cn/deg
EBI Genomes	EBI's collection of databases for the analysis of complete and unfinished viral , pro- and eukaryotic genomes	http://www.ebi.ac.uk/genomes
EGO	Eukaryotic gene orthologs: orthologous DNA sequences in the TIGR gene indices	http://www.tigr.org/tdb/tgi/ego/
EMGlib	Enhanced microbial genomes library: completely sequenced genomes of unicellular organisms	http://pbil.univ-lyon1.fr/emglib/emglib.html
Entrez Genomes	NCBI's collection of databases for the analysis of complete and unfinished viral , pro- and eukaryotic genomes	http://www.ncbi.nlm.nih.gov/entrez/ query.fcgi?db=Genome
ERGO	Light Integrated biochemical data on nine bacterial genomes: publicly available portion of the ERGO database	http://www.ergo-light.com/ERGO
FusionDB	Database of bacterial and archaeal gene fusion events	http://igs-server.cnrs-mrs.fr/FusionDB
Genome Atlas	DNA structural properties of sequenced genomes	http://www.cbs.dtu.dk/services/GenomeAtlas/
Genome Information Broker	DDBJ's collection of databases for the analysis of complete and unfinished viral , pro- and eukaryotic genomes	http://gib.genes.nig.ac.jp
Genome Reviews	Integrated view of complete genomes	http://www.ebi.ac.uk/GenomeReviews/
GOLD	Genomes online database: a listing of completed and ongoing genome projects	http://www.genomesonline.org/
HGT-DB	Putative horizontally transferred genes in prokaryotic genomes	http://www.fut.es/~debb/HGT/
Integr8	Functional classification of proteins in whole genomes	http://www.ebi.ac.uk/integr8/
KEGG	Kyoto encyclopedia of genes and genomes: integrated suite of databases on genes , proteins and metabolic pathways	http://www.genome.jp/kegg
MBGD	Microbial genome database for comparative analysis	http://mbgd.genome.ad.jp/
ORFanage	Database of orphan ORFs (ORFs with no homologs) in complete microbial genomes	http://www.cs.bgu.ac.il/~nomsiew/ORFans
PACRAT	Archaeal and bacterial intergenic sequence features	http://www.biosci.ohio-tate.edu/~pacrat
PartiGeneDB	Assembled partial genomes for _ 250 eukaryotic organisms	http://www.partigenedb.org/
PEDANT	Results of an automated analysis of genomic sequences	http://pedant.gsf.de/
TIGR Microbial Database	Lists of completed and ongoing genome projects with links to complete genome sequences	http://www.tigr.org/tdb/mdb/mdbcomplete.html
TIGR Comprehensive Microbial Resource	Various data on complete microbial genomes: uniform annotation, properties of DNA and predicted proteins	http://www.tigr.org/CMR
TransportDB	Predicted membrane transporters in complete genomes, classified according to the TC classification system	http://www.membranetransport.org/
WIT3	What is there ? Metabolic reconstruction for completely sequenced microbial genomes	http://www-wit.mcs.anl.gov/wit3/

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