Sequences Databases
English version of ABIM : Banques : séquences
- Databases (Databases, Multi-databases)
- Structural databases (BMRB, PDB, NRL ..)
- Nucleic acids (codon usage, Vectors, Tags, Transcription, Promotors, ARN ..)
- Proteins (Patterns, Alignments, Domains, Family, Organs, Pathology)
- Diverse (Databases, utilitaries ..)
- EMBL, Genbank, NRSub, SwissProt, PIR, PDB, OWL, PMD, TREMBL, GBNew, EMNew, ... with links : SRS system manual V.5, V.6, V.7
Please, consult periodically the lists of servers, databases and libraries
- SRS5
- EMBL, Heidelberg, Germany, - Data Banks
- Expasy, Geneva, Switzerland, - Data Banks
- IUBio, Indiana, USA, - Data Banks
- IVR, Kyoto, Japan, - Data Banks
- SRS6 or SRS7 (*) or SRS8 (**)
- BCGSC, Vancouver, Canada, - Data Banks *
- BCUP, Pune, India , - Data Banks *
- Ben,EMBNet, Belgium **
- Biocenter, Vienna, Austria **
- Bratislava, EMBNet, Slovak Republic **
- CBI, Beijing, China , - Data Banks *
- CBR-NRC, Halifax, Canada , - Data Banks
- CMB, EMBnet, Spain - Data Banks *
- Columbia, Columbia, USA - Data Banks *
- CSC, Espoo, Finland **
- DDBJ, Mishima, Japan , - Data Banks
- DKFZ, Heidelberg, Germany , - Data Banks *
- EBI, Hinxton, UK, -Data Banks *
- IBG, Bari, Italia, - Data Banks *
- ICG, Novosibirsk, Russia, - Data Banks
- ICPRO, London, UK, - Data Banks *
- IFOM, Milan, Italia, - Data Banks
- IMCAS, Beijing, China , - Data Banks *
- IGBMC, Strasbourg, France, - Data Banks *
- Institut Pasteur, Paris, France, - Data Banks *
- IUBio, Indiana, USA, - Data Banks
- IUBio, Indiana, USA, - Data Banks *
- PBIL, Lyon, France, - Data Banks
- NBIC, Amersfoort, the Netherlands, - Data Banks *
- NBN,Belleville, South Africa **
- PSNC, Poznan, Poland, - Data Banks *
- Sanger Centre, Hinxton, UK, - Data Banks *
- SCUT, Guangzhou, China, - Data Banks *
- WBW, Wageningen, the Netherlands, - Data Banks *
- WEHI, Australia, - Data Banks
- SRS 3D
- Genbank, SwissProt, PIR, PDB ...
- 3DinSight (PDB, EMBL, Swiss-Prot, Mutant, Pir ..) Riken (Search Tool for Structure, Function and Property of Biomolecules) (Japan)
- ACNUC www (EMBL, GenBank, NBRF, Hovergen, NRSub, HIDB, MGDB)
- BioThesaurus (thesaurus of protein and gene names) PIR (USA)
- CleanEx (attempts to merge and reorganize heterogeneous public gene expression profiles) ISREC (Switzerland)
- CluSTr (an automatic classification of UniProtKB proteins into groups of related proteins) EBI (UK)
- GenomeNet (Japon) www (DBGET)
- IDEAS (Integrated Database and Extended Analysis System for Nucleic Acids and Proteins) Kyoto (Japan)
- N.C.B.I. www
- Entrez (NCBI links with Medline) www, see also Cross-database
- RefSeq (aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for major research organisms) NCBI
- UniProt (Universal Protein Resource) EBI (UK), see also Expasy, see also PIR
- EMBL
- GenomeNet (Japon) www (DBGET)
- E.B.I (Cambridge) www
- SRS : all the [SRS] servers, also available EMNEW
- EXProt (database for EXPerimentally verified Protein functions)
- GenBank
- GenomeNet (Japon) www (DBGET)
- NCBI www, Inherited Disease Genes Identified by Positional Cloning, see also Genome Survey Sequence dbGSS, see also HTGS
- XPRO (database of eukaryotic protein-encoding DNA sequences in GenBank) NUS (Singapore)
- SRS : all the [SRS] servers, except EBI, Sanger
- Gene Ontology
- FatiGO - Data mining with Gene Ontology Valencia (Spain)
- Gene Ontology Consortium GO
- GO PaD (the Gene Ontology Partition Database) Harvard (USA)
- GOstat (find statistically overrepresented Gene Ontologies within a group of genes) Wehi (Australia)
- QuickGO GO Browser EBI (UK)
- Hovergen
- IMGT (ImMunoGeneTics database)
- An integrated database for immunogenetics IMGT (It combines nucleotide and protein sequences of immunoglobulins, T-cell receptors (LIGM-DB) and HLA molecules (HLA-DB) and Dnaplot) - (Montpellier France)
- IMGT : mirror (incomplete) Cologne (Dnaplot : Analyse Human Immunoglobulin Genes using the V BASE) (Allemagne)
- IMGT at EBI EBI (Dnaplot : Analyse Human and mouse Immunoglobulin Genes, analyse T cell receptor sequences) (UK)
- IMGT/HLA EBI (UK)
- SRS : at EMBL-EBI (UK)
- Kabat Sequence Database
- Mutations
- Cystic Fibrosis Mutation Data Base Toronto (Canada)
- Mutation Database Web server Melbourne (Australia), see also EBI (UK)
- PMD (Protein Mutants Database) SRS(Heidelberg), see also Osaka (Japan), see also NIG (Japan)
- OWL (Non redundant protein database)
- OWL (London) www
- Database Browser (OWL, PRINTS, ALIGN, GPCR, CATH, PDBsum) UCL (UK)
- Database Information Retriever (OWL, PRINTS) Manchester (UK)
- SRS : at ICPRO (UK)
- PIR
- GenomeNet (Japon) www (DBGET)
- iProClass Georgetown (USA)
- PIR Georgetown (USA)
- PIR-PSD PIR (USA)
- PIRSF (family classification system) Georgetown (USA)
- RESID (database of protein post-translational modifications) EBI (UK)
- SRS : all the [SRS] servers
- REPBASE
- SRS : (linked libraries : REPBASE) : EBI
- SwissProt
- AllAllDB CBRG (Switzerland)
- GenomeNet (Japon) www (DBGET)
- E.B.I (Cambridge) www
- Expasy www : search by description, accession number, author, citation, full text, see also nomenclature documents and Swiss-Shop (sequence allerting system that allows you to automatically obtain new sequence entries relevant to your field(s) of interest)
- dbPTM (an information repository of protein post-translational modification) Hsin-Chu (Taiwan)
- PDBSprotEC (Web-accessible database linking PDB chains to EC numbers via SwissProt) Whiteknights (UK)
- ProtoMap (An automatic hierarchical classification of all SWISSPROT proteins) Cornell (USA)
- ProtoNet (ahierarchical classification of one million protein sequences : SwissProt and TrEMBL) Jerusalem (Israel)
- Randomly retrieve a SWISS-PROT/TREMBL entry Expasy
- SIRW (Simple Indexing and Retrieval System : Swissprot, Prosite, SpTrembl, Enzyme, Sprot) EMBL (Germany)
- Taxonomy browser (Newt) EBI (UK)
- SRS : all the [SRS] servers, also available SWISSNEW
- SYFPEITHI
- Database of MHC ligands and peptide motifs Tuebingen (Germany)
- TREMBL (CDS features from EMBL as translated peptide sequences)
- SRS : at PBIL (France), EBI (EBI) also available TREMBLNEW
- Database of Macromolecular Movements Yale (USA)
- 3MOTIF (visualizing conserved protein sequence motifs in the protein structure database) Stanford (USA)
- SitesBase (a database for structure-based protein-ligand binding site comparisons) Leeds (UK)
- Structure BMCD
- Structure BMRB
- BMRB Wisconsin (USA)
- WWW Database Gateway to BioMagResBank (NIH) : links with PDB, PIR, SwissProt
- Structure MMDB
- Molecular Modelling Database NCBI (USA)
- Entrez structure NCBI (USA)
- PDBeast (Taxonomy in MMDB) NCBI (USA)
- Structure PDB
- wwPDB
- 3 Dee - Database of Protein Domain Definitions Dundee (UK)
- 3D Lectin database CERMAV (French)
- 3DinSight Riken (Search Tool for Structure, Function and Property of Biomolecules) (Japan)
- 3DB Browser
- OCA
- Brookhaven RCSB
- Brookhaven : mirror at EBI, ICM (Poland), Rehovot (Israel)
- Database Browser (OWL, PRINTS, ALIGN, GPCR, CATH, PDBsum) UCL (UK)
- PDBsum (an at-a-glance overview of every macromolecular structure) EBI (UK)
- AffinDB (a freely accessible database of affinities for protein-ligand complexes from the PDB) Marburg (Germany)
- Antibody Structures in the Protein Databank Whiteknights (UK)
- CSS (analysis of carbohydrate 3D structures derived from the PDB) Heidelberg (Germany)
- BSM (UK) Enzyme Structures Database www (a subset)
- Dali database Helsinki (Finland)
- Database of Structural Motifs in Proteins CDFD (India)
- DisProt (a database of protein disorder) Indiana (USA)
- PDBSite (database of the 3D structure of protein functional sites) Novosibirsk (Russian)
- EBI (Cambridge) SRS (links with HSSP, DSSP and FSSP)
- eF-site and PDBjViewer (database and viewer for protein functional sites) Yokohama (Japan)
- EMBL (Heidelberg) SRS
- EMBL links with HSSP (SRS)
- Fetch a PDB entry Pasteur (French)
- FireDB (a database of functionally important residues from proteins of known structure) Madrid (Spain)
- FSN - Flexible Structural Neighborhood (a database of protein structural similarities and alignments) La Jolla (USA)
- Functional Classifier San Diego (USA)
- GenomeNet (Japon) www (DBGET)
- GTD (Genomic Threading Database : structural annotations of proteomes, translated from the genomes of key organisms - PDB, SCOP, MD5) London (UK)
- HIC-Up (hetero-compounds encountered in PDB) Uppsala (Sweden)
- iGNM (protein functional motions based on Gaussian Network Model) Pittsburgh (USA)
- Macromolecular Structure Database (PDB, 3Dseq, PQS, NDB, etc..) EBI (UK)
- Macromolecular Object Oriented Search Engine Moose (USA)
- Mapping PDB chains to UniProtKB entries London (UK)
- Membrane Proteins (PDB_id) Irvine (USA)
- MODBASE (Comparative Protein Structure Models) UCSF (USA)
- MutaProt (Comparison of PDB files which differ by point mutations) Weizmann (Israel)
- NIH : Molecules R US Utility www, see also "at a glance" (classification function, organism ..)
- PDBSprotEC (Web-accessible database linking PDB chains to EC numbers via SwissProt) Whiteknights (UK)
- PDBsum EBI (UK)
- Phospho3D (database of three-dimensional structures of protein phosphorylation sites) Rome (Italy)
- PISCE (recent improvements to a PDB sequence culling server) Philadelphia (USA)
- ProMode (database of normal mode analysis of proteins) Tokyo (Japan)
- ProSAT (Protein Structure Annotation Tool) Heidelberg (Germany)
- RCSB PDB information portal for structural genomics Rutgers (USA)
- UCL (London) : antibody and light chain dimer structures currently available in PDB
- Protein Motions Database Yale (USA)
- Structure NRL-3D
- Structure NDB
- ATLAS of Nucleic Acid Containing Structures Rutgers (USA)
- Nucleic Acid Database Rutgers (USA)
- Structure RELIBase
- Structural data about receptor/ligand complexes EBI (UK) ("Java viewer" and "VRML Helper" required), see also Rutgers
- Structure PASTA
- Protein Active Site Template Acquisition Sheffield (UK)
- Structure PIBASE
- A comprehensive database of structurally defined protein interfaces California (USA)
- Structure PIDD
- Database for Protein Inter-atomic Distance Distributions Iowa (USA)
- Structure PMDB
- Manually built 3D models of proteins Rome (Italie)
- Structure PROCAT
- Database of 3D enzyme active site templates UCL (UK)
- Structure SESAM
- A database for protein structures UCMB (Belgium)
- Structure SLoop
- Database of Super Secondary Fragments Cambridge (UK)
- Codons usage
- Vectors - Oligo
- PlasmID (a centralized repository for plasmid clone information and distribution) Cambridge (USA)
- VectorDB (Phages, plasmids, cosmids, virus, YAC ...) Stanford (USA)
- SRS - VECTOR : BEN, (Brussels)
- Tags
- Mendel-ESTS MBG (UK)
- Expressed sequences (dbEST - NCBI) www mirror at EBI
- Sites (dbSTS - NCBI) www miroir à EBI
- STACK (Sequence Tag Alignment and Consensus Knowledgebase) SANBI (South Africa)
- TBestDB (a taxonomically broad database of expressed sequence tags (ESTs)) Montreal (Canada)
- UniSTS (sequence tagged sites (STSs) derived from STS-based maps and other experiments) NCBI (USA)
- SRS (DBEST, DBESTNEW) : CSC (Finland) (+ DBSTS, DBSTSNEW), WEHI (Australia)
- Eucaryotic promotors
- EPD Database ISREC (Switzerland)
- SRS (linked libraries : EPD) : all the [SRS] servers
- Transcription - Translation Factors
- RNA
- 5'-UTR and 3'-UTR of eukaryotic mRNAs Bari (Italy)
- Aptamer (DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules) Texas (USA)
- Base pair classification Montreal (Canada)
- Database of non-coding RNAs Poznan (Poland)
- Database of ribosomal crosslinks Berlin (Germany)
- Databases of small and large ribosomal subunit RNA sequences (European ribosomal RNA database) Gent (Belgium)
- dbRES (database for annotated RNA editing sites) Beijing (China)
- EID (Exon-Intron Database) Ohio (USA)
- fRNAdb (a platform for mining/annotating functional RNA candidates from non-coding RNA sequences) Tokyo (Japan)
- FUGOID (Functional Genomics of Organelle Introns) Texas (USA)
- Genecensus (LSU rRNA _ 8 SSU rRNA _20 SSU rRNA, Tree) Yale (USA)
- Genomic tRNA Database (GtRDB) Washington (USA)
- Internal Ribosome Entry Sites (IRES) Toulouse (French)
- Intron- Exon Knowledge Base Singapore, see also < A HREF="http://sege.ntu.edu.sg/wester/exint/">ExInt
- Intron Sequence and Information database Isis, another link (USA)
- Intron statistics Trieste (Italy)
- MeRNA (a database of metal ion binding sites in RNA structures) Berkeley (USA)
- MIDB (Eukaryotic Mismatched Intron Database) NUS (Singapore)
- miRBase Sanger (UK)
- miRNAMap (genomic maps of microRNA genes and their target genes in mammalian genomes) Hsin-Chu (Taiwan)
- Mobile Group II Introns Database Calgary (Canada)
- MODOMICS (a database of RNA modification pathways) Warsaw (Poland)
- NATsDB (Natural Antisense Transcripts DataBase) Beijing (China)
- ncRNAdb (non coding RNAs database) Poznan (Poland)
- Non-Canonical Base Pair Database Houston (USA)
- Noncoding RNAs Database Poznan (Poland)
- ncRNA (RNAdb : a comprehensive mammalian noncoding RNA database) Queensland (Australia)
- NONCODE (an integrated knowledge database of non-coding RNAs) Beijing (China)
- NPIDB (database of Nucleic Acids-Protein Interactions) Moscow (Russia)
- NPInter (the noncoding RNAs and protein related biomacromolecules interaction database) Beijing (China)
- PACdb (PolyA Cleavage Site and 3'-UTR Database) Jackson (USA), see also AtPACdb (for Arabidopsis thaliana)
- probeBase (resource for rRNA-targeted oligonucleotide probes) Wien (Austria)
- Prokaryotic 16s rRNA signature database Houston (USA)
- PseudoBase (collection of RNA pseudoknots) Leiden (the Netherlands)
- qPrimerDepot (a primer database for quantitative real time PCR) Baltimore (USA)
- RAD (RNA Abundance Database) CBIL (USA)
- RAG (RNA as graphs database) New York (USA)
- RAPAD (RNA and Protein Abundance Database) Glasgow (UK)
- RDP The Ribosomal Database Project CME (USA)
- RDP Classification Server UTHCT
- RPG (ribosomal protein gene database) Miyazaki (Japan)
- REDIdb (the RNA editing database) Calabria (Italy)
- Rfam (non-coding RNA families) Sanger (UK), see also Washington (USA)
- Ribosomal RNA Mutational Database FMC (USA)
- 5S rRNA Poznan
- RNA Editing Web Site UCLA (USA)
- RNAi (small inhibitory RNAs against human and mouse genes) MIT (USA)
- RNAi Codex (a portal/database for short-hairpin RNA (shRNA) gene-silencing constructs) CSH (USA)
- RNA interference ressources Ambion (USA)
- The RNA Modification Database Utah
- SCOR (structural classification of RNA) LBL (USA)
- SEDB (structural exon database, mapping exon boundaries on multiple protein structures) Boston (USA)
- SEGE (A database on intron less/single exonic genes from eukaryotes) LICR (USA)
- SELEX DB (high affinity DNA and RNA sequences) EMBNet (Russian)
- siRecords (an extensive database of mammalian siRNAs with efficacy ratings) Minnesota (USA)
- snoRNA-LBME-db (a comprehensive database of human H/ACA and C/D box snoRNAs) Toulouse (French)
- Sno/scaRNAbase (a curated database for small nucleolar RNAs and cajal body-specific RNAs) Shanghai (China)
- RNA Structure Database Rnabase (USA)
- SRPDB (Signal Recognition Particle Database) UTHCT
- SSU rRNA Modification Database Utah (USA)
- tmRNA database (earlier called "10S RNA")) UTHCT, see also Indiana (USA), see also Aarhus (Denmark)
- tmRNA (reductive evolution of tmRNA in plastids and other endosymbionts) Indiana (USA)
- snoRNA Database (2'-O-ribose methylation) California (USA)
- U12DB (a database of orthologous U12-type spliceosomal introns) Barcelona (Spain)
- Specific sites
- S/MARt DB (S/MAR transaction DataBase) Goettingen (Germany)
- TassDB (a database of alternative tandem splice sites) Freiburg (Germany)
- Others
- ACUTS (Compilation of Ancient Conserved UnTranslated Sequences) ACNUC (France)
- DDBJ (DNA Data Bank of Japan) NIG (Japan)
- DNA reference alignment benchmarks based on tertiary structure of encoded proteins Utah (USA)
- Probe (molecules that complement a specific mRNA or DNA sequence) NCBI (USA)
- Short repeated palindromes in enterobacteria Pasteur (French)
- Protein patterns, sites, alignments
- Alignments (protein family)
- 3D_Ali (A database of aligned protein structures and related sequences) EMBL (Germany)
- CAMPASS (CAMbridge database of Proteii Alignments organised as Structural Superfamilies) Cambridge (UK), see also NCBS (India), see also Conservation of secondary structure elements in protein superfamilies SSDB
- CluSTr (an automatic classification of UniProtKB proteins into groups of related proteins) EBI (UK)
- DAPS (Database of Aligned Protein Structures) DOE-MBI (USA)
- Database Browser (OWL, PRINTS, ALIGN, GPCR, CATH, PDBsum) UCL (UK)
- DBAli (database of sequence alignments) UCSF (USA)
- DMAPS (database of multiple alignments for protein structures) Albany (USA)
- eBLOCKs (enumerating conserved protein blocks to achieve maximal sensitivity and specificity) Stanford (USA)
- FPSPD (sequence patterns derived from the automated prediction of functional residues in structurally-aligned homologous protein families) Cambridge (UK)
- FSN - Flexible Structural Neighborhood (a database of protein structural similarities and alignments) La Jolla (USA)
- Homologous Structure Alignment Database Cambridge (UK), another link
- MulPSSM (a database of multiple position-specific scoring matrices of protein domain families) Bangalore (India)
- PALI (Phylogeny and ALIgnment of homologous protein structures) CSBG (India)
- Phylogeny of the Unicellular Organisms Metabolic Pathways Alignments WIT (Argonne) (interconnnected metabolic pathways, multiple protein sequence alignments, their phylogenetic trees and other information associated with each alignment)
- ProtBuD (a database of biological unit structures of protein families and superfamilies) Philadelphia (USA)
- SIMAP (the similarity matrix of proteins) MIPS (Germany)
- SISYPHUS (structural alignments for proteins with non-trivial relationships) Cambridge (UK)
- TOPOFIT-DB (a database of protein structural alignments based on the TOPOFIT method) Boston (USA)
- SRS (linked libraries : PRINTS) : see the [SRS] servers
- BLOCKS
- Hutchinson Cancer Research Center www, mirror at Weizmann Institute
- SRS (linked libraries : BLOCKS) : see the [SRS] servers
- CoPS (Comprehensive Peptide Signature Database) Delhi (India)
- HSSP (homology-derived structures of proteins)
- EBI (UK)
- SRS (libraries with protein structure information : HSSP) : at EBI (England)
- Interactions
- 3did (interacting protein domains of known three-dimensional structure) EMBL (Germany)
- AANT (Amino Acid-Nucleotide Interaction Database) Texas (USA)
- ABAC Database (equivalent binding sites reveal convergently evolved interaction motifs) Dresden (Germany)
- Adan (protein-protein interaction of modular domains) EMBL (Germany)
- Aptamer (DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules) Texas (USA)
- BIND (biomolecular interaction network database) Toronto (Canada)
- BindingDB (database of experimentally determined protein-ligand binding affinities) Maryland (USA)
- BioGRID (a general repository for interaction datasets) Toronto (Canada)
- DIP (Database of Interacting Proteins) UCLA (USA)
- DOMINO (a database of domain-peptide interactions) Rome (Italy)
- GRID Database (Genetic and Physical Interactions) SLRI (Canada)
- ICBS (database of interactions between protein chains mediated by beta-sheet formation) Irvine (USA)
- iMOTdb (collection of spatially interacting motifs in proteins) Bangalore (India)
- InterDom (database of putative interacting protein domains) Singapore
- IntAct (an open source molecular interaction database) EBI (UK)
- LigBase (Structural Database of Aligned Ligand Binding Sites) UCSF (USA)
- MiMi (Michigan molecular interacitions) Michigan (USA)
- MINT (Molecular Interaction database) CBM (Italy)
- MPPI (Mammalian Protein-Protein Interaction Database) MIPS (Germany)
- NPInter (the noncoding RNAs and protein related biomacromolecules interaction database) Beijing (China)
- PDZBase (a protein-protein interaction database for PDZ-domains) Cornell (USA)
- PIBASE (a comprehensive database of structurally defined protein interfaces) UCSF (USA)
- PINT (protein-protein Interactions thermodynamic database) Fukuoka (Japan)
- PRECISE (database of Predicted and Consensus Interaction Sites in Enzymes) Boston (USA)
- Prodistin (functional classification of proteins based on interactions) Marseille (French)
- Protein-Protein Interaction Jena (Germany)
- PSIMAP (database of protein structural interactome map) Daejeon (Korea), another link
- Q-SiteFinder (an energy-based method for the prediction of protein-ligand binding sites) Leeds (UK)
- SNAPPI-DB (a database and API of Structures, iNterfaces and Alignments for Protein-Protein Interactions) Dundee (Scotland)
- STRING (known and predicted protein-protein associations, integrated and transferred across organisms) EMBL (Germany)
- UniHI (an entry gate to the human protein interactome) Berlin (Germany)
- MotifDic
- Search MotifDic database using DBGET (Prosite, Blocks, Prints, Prodom, Pfam) Kyoto (Japan)
- ProClass Database
- Prosite
- GenomeNet (Japon) www (DBGET)
- E.B.I (Interpro) www
- Expasy www
- SRS (linked libraries : PROSITE) : all the [SRS] servers, also available PROSITEDOC (dictionary)
- Protein Motif Fingerprint Database
- Domains
- ADDA (a domain database with global coverage of the protein universe) Helsinki (Finland)
- ArchDB (compilation of structural classifications of loops extracted from known protein structures) Barcelona (Spain)
- Catalytic Site Atlas (enzyme active sites and catalytic residues in enzymes of 3D structure) EBI (UK)
- CDART (Conserved Domain Architecture Retrieval Tool) NCBI (USA)
- CDD (Conserved Domain Database) NCBI, see also Entrez (USA)
- COGs (Clusters of Orthologous Groups NCBI (USA)
- DIAL (automatic identification of structural domains in proteins) Tamilnadu (India)
- DomIns (domain insertions in known protein structures) MRC (UK)
- Epitome (database of structurally inferred antigenic epitopes in proteins) Columbia (USA)
- EVEREST (a collection of evolutionary conserved protein domains) Jerusalem (Israel)
- Hits Home (database devoted to protein domains) SIB_ISREC (Switzerland)
- InterPro (Integrated Resource of Protein Domain and Functional Sites) EBI (UK)
- PDBSite (database of the 3D structure of protein functional sites) Novosibirsk (Russian)
- PhosphoBase (database of experimentally verified phosphorylation sites) CBS
- Phosphorylation site database Virginia (USA)
- PRODOC (a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families) Bangalore (India)
- PROF_ PAT 1.3 (Updated database of patterns used to detect local similarities) ICG (Russian)
- PRODOM
- PRODOM Toulouse (French)
- SRS (linked libraries : PRODOM) [SRS] servers
- ProtBuD (a database of biological unit structures of protein families and superfamilies) Philadelphia (USA)
- PROTCOM (searchable database of protein complexes enhanced with domain-domain structures) Clemson (USA)
- SBASE
- SMART (annotation of protein domains and the analysis of domain architectures) Heidelberg (Germany)
- SURFACE (database of protein surface patches, defined as putative surface functional sites) Rome (Italy)
- Proteins - Genes Family
- Gene Family Database (Mendel-GFDb) MBG (UK)
- PANTHER (database of protein families, subfamilies, functions and pathways) Applied Biosystems (USA)
- Pfam (collection of protein domain families > 1488) Sanger, see also Washington, see also Karolinska, see also INRA
- Pfam : FunShift (database of function shift analysis on protein subfamilies) Stockholm (Sweden)
- Pfam : taxonomy query Sanger (UK)
- iPfam (visualization of protein-protein interactions in PDB at domain and amino acid resolutions) Sanger (UK)
- Allergen sequences (IgE-mediated atopic allergies in humans) Expasy (SwissProt)
- Allergen Sequence Database Illinois (USA)
- The AAA protein superfamily (ATPases Associated with various cellular Activities) Graz (Austria)
- ABC-transporter genes (human) Wageningen (The Netherlands)
- ABC transporter (Arabidopsis) TAIR (USA)
- ABCISSE (ATP Binding Cassette) Pasteur (French)
- ADME-AP (Drug ADME associated proteins) Singapore
- Aldehyde Dehydrogenase Gene Superfamily Database (ALDH-GSD) UCHSC (USA)
- Aldo-Keto Reductase (AKR) superfamily Pennsylvania (USA)
- Aminoacyl tRNA synthetases list Expasy
- Aminoacyl-tRNA Synthetase Data Bank (AARSDB) Poznan (Poland)
- Androgen receptor gene mutations database Montreal (Canada)
- ANTIMIC (a database of antimicrobial sequences) IIR (Singapore)
- AntiMicrobial Sequences Database AMSdb (Italy)
- APD (the Antimicrobial Peptide Database) Nebraska (USA)
- Apoptosis regulators Michigan (USA)
- Arabidopsis Beta-glucosidases and galactosidases Iowa (USA)
- ASC (collection of Active protein Sequences, or protein fragments or subsequences, collected in the form of function-oriented databases) Roma (Italy)
- ATPase database (P-type) Copenhagen (Denmark)
- Bacterial lipoproteins (DOLOP) MRC (UK)
- Blood group antigen proteins Expasy
- Carbohydrate-Active Enzymes CAZY (France)
- The Chaperonin Home Page UTHSC
- CD antigens in SWISS-PROT Expasy
- CD PROW (Protein Reviews On The Web) NCBI
- Collagen : human type I collagen gene mutations Leicester (UK)
- COMPEL (composite regulatory elements affecting gene transcription in eukaryotes) ICG (Russian)
- Conopeptide sequences and structures Queensland (Australia)
- CREMOFAC (database of chromatin remodeling factors) Bangalore (India)
- CSD (database for Cold Shock Domain) Marburg (Germany)
- Cytochrome P-450 (ICGEB Trieste) www, mirror at Budapest
- Cytochrome P450 2E1 UCHSC (USA)
- Cytokine Family cDNA Database Kumamoto (Japan)
- Cytokines Online Pathfinder Encyclopaedia COPE (Germany)
- Cystathionine Beta Synthase Sanger (UK)
- Defensins (a manually curated database and information source focused on the defensins family of antimicrobial peptides) Singapore
- DExH/D proteins (subgroup of the Superfamily 2 (SF2) helicases) Columbia (USA)
- DNA-binding sites of Tc1, mariner and pogo transposases Weizmann (Israel)
- DNA-Proteins interactions db (DPInteract) Harvard (USA)
- DynDom (database of protein domain motions) Norwich (UK)
- EF-hand calcium-binding proteins db (CABP) Scripps (USA)
- Eph Receptor Tyrosine Kinases Washington (USA)
- EPIMHC (a curated database of MHC-binding peptides for customized computational vaccinology) Harvard (USA)
- Epoxide hydrolase and haloalkane dehalogenase Stuttgart (Germany)
- ERGDB (Estrogen Responsive Genes Database) KELIIR (Singapore)
- Erythropoiesis database (EpoDB) CBIL (USA)
- eSLDB (eukaryotic subcellular localization database) Bologna (Italy)
- ESTerase and a/b Hydrolase Relatives (CHEDB) : superfamily of alpha/beta hydrolase which are homologous to cholinesterases INRA (Montpellier), another link
- Estrogen receptor resource Georgetown (USA)
- Expansin PennState (USA)
- EyeSite (a semi-automated database of protein families in the eye) Birbeck (UK)
- Factor VIII HAMSTeRS (UK)
- FAD-dependent pyridine nucleotide oxidoreductases ICGEB (Italy)
- Flavodoxins ICGEB (Italy)
- FYVE finger proteins Bergen (Norway)
- GeneNet (groups of coordinately working genes) Novosibirsk (Russian)
- GLIDA (GPCR-ligand database for chemical genomic drug discovery) Kyoto (Japan)
- Globins (Pennsylvania State University) www
- Glucocorticoid Receptor Resource Georgetown (USA)
- Glucose-6-Phosphate Dehydrogenase (G6PD) deficiency G6PD (USA), see also RUBiC (UK)
- Glycosyl hydrolases Expasy
- Gonadotropin-releasing hormone (GnRH) TIGR (USA)
- GPCR finger PRINTS Manchester (UK)
- Haemophilia B Mutation Database KCL (UK)
- HCS (hierarchical classification of hydrolases catalytic sites) Moscow (Russia)
- Hera (human endoplasmic reticulum resident proteins database) Montreal (Canada)
- Histone Sequence Database NHGRI-NCBI (USA)
- Homeodomain Resource NHGRI (USA)
- HOX database IEPHB, see also Expasy
- Human Olfactory Receptor Weizmann (Israel)
- Human plasma membrane receptome Stanford (USA)
- IMGT
- An integrated database for immunogenetics Cologne (Dnaplot : Analyse Human Immunoglobulin Genes using the V BASE) (Germany)
- An integrated database for immunogenetics IMGT (It combines nucleotide and protein sequences of immunoglobulins, T-cell receptors (LIGM-DB) and HLA molecules (HLA-DB)) - (CNUSC France)
- An integrated database for immunogenetics EBI (UK)
- SRS : at EMBL-EBI (England)
- JenPep (peptides binding to MHC class I, II and TAP molecules) EJIVR (UK)
- Protéines kinase (PKR) SDSC (USA), see also Sugen
- KSD (Kinase Sequence Database) UCSF (USA)
- Kinesin (mechanochemical protein) FHCRC (USA)
- KinG (database of protein kinases in genomes) Bangalore (India)
- KNOTTIN (knottins or inhibitor cystine knots, small disulfide-rich proteins with a knotted topology) CBS (French)
- L1CAM (Neuronal cell adhesion molecule : domains, mutations, sequences) Groningen (The Netherlands)
- Ligand-Gated Ion Channels database (manually curated) EBI (UK)
- Lipase Engineering Database Stuttgart (Germany)
- LOCATE (a mouse protein subcellular localization database) Queensland (Australia)
- LOX-DB (lipoxygenases database) Heidelberg (Germany)
- LOChom (database of predicted subcellular localization based on sequence homology) Columbia (USA), see also LOC3d
- MAPPER (putative transcription factor binding sites in multiple genomes) Boston (USA)
- MeTaDoR (a comprehensive resource for membrane targeting domains and their host proteins) Chicago (USA)
- Metalloprotein DataBase SRI (USA)
- Metallothionein Zurich (Switzerland), see also index of MT Expasy
- MHC binding peptides WEHI (Australia)
- MHC human database NCBI (USA)
- MiGenes (a searchable interspecies database of mitochondrial proteins curated using gene ontology annotation) New York (USA)
- Mammalian mitochondrial tRNA genes Strasbourg (French)
- MitoDat : Mendelian Inheritance and the Mitochondrion database NCI
- Muscle-Specific Regulation of Transcription (MTIR) CBIL (USA)
- MutS TIGR (USA)
- Myosin MRC-LMB (UK), mirror at ProWeb
- NESbase (proteins in which the presence of Leucine-rich nuclear export signal (NES) has been experimentally verified) CBS (Denmark)
- Neuronal Database Yale (USA)
- Neurotransmitter receptors (Neuron DB) Yale (USA)
- Neurotrophic Factors Birkbeck (UK)
- Nicotinica Encyclopaedia (nicotinic acetylcholine receptors) Pasteur (France)
- NLSdb (nuclear localization signals) Columbia (USA)
- NMP-db (nuclear matrix associated proteins) Columbia (USA), another link
- NOPdb (nucleolar oroteome database) Dundee (UK)
- Nuclear Protein Database (NPD) MRC (UK)
- NucleaRDB: a Federated Database for Nuclear Receptors UCSF (USA)
- Nuclear Receptor Resource (NRR : Glucocorticoid, Thyroid hormone, Androgen, Mineralocorticoid receptors) Georgetown (USA)
- NuReBase (Nuclear Receptor dataBase) Lyon (French)
- NURSA (hyperlinking the nuclear receptor signaling community) Texas (USA)
- O-glycosylated proteins database O-GlycBase (Denmark)
- Olfactory Receptor DataBase Yale
- Ovarian Kaleidoscope Database (OKDB) Stanford (USA)
- P53 (Structure, expression, modifications...) Curie (French)
- P53 mutations database Tokyo (Japan), see also Prague
- P53 mutations in human tumors and cell lines IARC (France)
- Pandit (protein and associated nucleotide domains with inferred trees) EBI (UK)
- Panther (mRNA/protein expression analysis and coding SNP scoring tools) California (USA)
- PAX6 mutation database (Paired Box Homeotic Gene 6) MRC (UK)
- Peptaibol Birkbeck (UK)
- Peptidases Expasy (SwissProt)
- Peptidases (Merops) Sanger (UK), see also Prolysis (French)
- Peroxidase (plant) Geneva (Switzerland)
- Phenylalanine hydroxylase PAH (Canada)
- Phosphabase (phosphatases) Manchester (UK)
- Phosphodiesterase Washington (USA)
- Phosphoprotein Database (PPDB) NCI (USA)
- Phytochromes Jena (Germany)
- PIN (proteins interacting in nucleus) New York (USA)
- Plant-PI (plant protease inhibitor) Bari (Italy)
- PlasmaDB (Human Plasma Database) NCI (USA)
- PLPMDB (Pyridoxal-5'-phosphate dependent enzymes mutation database) Roma (Italy)
- PPAR (Peroxisome Proliferator-Activated Receptor Resource) Pennsylvania (USA)
- Predicted sigma54-dependent promoters (by organism) Southampton (UK)
- Promise (Prosthetic groups and Metal Ions in Protein Active Sites Database) SRI (USA)
- Proteins Domains (FHA, Death, PLD, G-protein, UBA, UBX) ISREC, see also Hits
- Protein Family TIGR (USA)
- Protein Family Cores Stanford (USA)
- Proteases and inhibitors Prolysis (France)
- G protein-Coupled Receptor NIH, see also list in SwissProt, see also "G P C R pattern recognition" UCL (UK), see also GPCR
- RecA protein family TIGR (USA)
- Repair-FunMap (a functional database of proteins of the DNA repair systems) Philadelphia (USA)
- Restriction enzymes and methylases entries Expasy (SwissProt)
- The Ribonuclease P Database North Carolina
- Ribosomal Proteins Families Expasy (SwissProt)
- Scorpion toxin Singapore
- Sentra (database of signal transduction proteins for comparative genome analysis) Argonne (USA)
- Serine protease Washington (USA)
- Signaling PAthway Database SPAD (Japan)
- Snake neurotoxin database Singapore
- SNP@Domain (resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences) Daejeon (Corée)
- SNF2 family of proteins TIGR (USA)
- STCDB (signal transduction classification) Bielefeld (Germany)
- Steroid Receptor Associated Proteins Resource Ohio (USA)
- SubLoc (database of protein subcellular localization) Beijing (China)
- SUPFAM (homologous families in Pfam and PALI) CSBG (India)
- SYSTERS (Protein Family Database) Max-Planck (Germany)
- TargetDB (peptides targeting proteins to cellular locations) NMSU (USA)
- TCDB (Database for membrane transport protein analyses and information) UCSD (USA)
- THGS (a database of transmembrane helices in genome sequences) Bangalore (India)
- TMPDB (transMembrane protein database) Hirosaki (Japon)
- Topoisomerase (Gyr b) ICB (Japan)
- TRAIT (transcripts expressed in human skeletal muscle) Padua (Italy)
- Transcription factor sites (E. Coli) Wadsworth (USA)
- Translation Initiation Factor : list at Expasy
- Transmembrane proteins (PDBTM) Budapest (Hungary)
- TransportDB (a relational database of cellular membrane transport systems) Rockville (USA)
- Transport proteins families San Diego (USA)
- tRNA sequences and genes Bayreuth (Germany)
- TRRD (Transcription regulatory region) ICG (Russian)
- TSGDB (tumor suppressor gene database) Los Angeles (USA)
- UvrA (ABC (ATP binding cassette) superfamily of proteins) TIGR (USA)
- Venom composition Melbourne (Australia)
- Venom and toxin Melbourne (Australia)
- Vitamin D Nuclear Receptor (VDR) Boston (USA)
- von Willebrand Factor Database Sheffield (UK)
- Wnt genes Stanford (USA)
- UPF (Uncharacterized Protein Families) Expasy
- WD-repeat Family (tryptophan-aspartate repeat) BMERC (USA)
- YTPdb (Yeast Transport Protein db) ULB (Belgium)
- Structural classification of proteins
- 3D-GENOMICS (database to compare structural and functional annotations of proteins between sequenced genomes) London (UK)
- CATH (London) UCL
- CyBase (a database of cyclic protein sequence and structure) Queensland (Australia)
- Database Browser (OWL, PRINTS, ALIGN, GPCR, CATH, PDBsum) UCL (UK)
- DHS (dictionary of homologous superfamilies, built on CATH) London (UK)
- MinSet (a general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database) London (UK)
- QSCOP (SCOP quantified by structural relationships) Salzburg (Austria)
- SCOP (Cambridge) www, see also Berkeley, see also Wehi
- SCOPPI (a structural classification of protein-protein interfaces) Dresden (Germany)
- Superfamily (Hidden Markov Models) Cambridge (UK)
- TOPS (an enhanced database of protein structural topology) Leeds (UK)
- Pathology
- ALPSbase : Database of mutations causing human ALPS NHGRI-NIH (USA)
- Androgen Receptor Mutations Database Montreal (Canada)
- Angiogenesis related disease database Seoul (Republic of Korea)
- BCI Databases (Tumor, Breast cancer, Mamary transgene, GPCR list) BCI (USA), see also BCF
- BIOMDB (Database of mutations causing tetrahydrobiopterin deficiencies) Zurich (Switzerland)
- Breast Cancer Gene Database BCM (USA)
- BTKbase: Mutation registry for X-linked agammaglobulinemia Helsinki (Finland)
- Connexin-deafness IRO (Spain)
- CD40L Defect Database (leads to X-linked Hyper-IgM syndrome) Expasy
- CGAP (Cancer Genome Anatomy Project) NCI-NCBI (USA)
- DNA Patent Database DPD (USA)
- Fibrillin1 gene mutations implicated in Marfan Syndrome Necker (France)
- GENDIAG (Genetic syndroms and development : included in Orphanet) Paris (France)
- KinMutBase (disease-causing mutations in protein kinase domains) Helsinki (Finland)
- LDLR gene in familial hypercholesterolemia UCL (England)
- OCRL1 Mutations Causing Lowe Syndrome NHGRI-NIH (USA)
- ORPHANET (rare diseases and orphan drugs) Paris (French)
- PEDB (Prostate database) FHCRC (USA)
- PharmGED (pharmacogenetic effect database) Singapore
- TGD : Tumor Gene Database BCM (database of genes associated with tumorigenesis and cellular transformation)
- Diverse
- AGML Central (web based gel proteomic infrastructure) South Carolina (USA)
- AliasServer (a web server to handle multiple aliases used to refer to proteins) Bordeaux (French)
- aMAZE (relational database, which contains information on gene expression, catalysed chemical reactions, regulatory interactions, protein assembly, as well as metabolic and signal transduction pathways) Louvain (Belgium)
- ASEdb (database of alanine mutations and their effects on the free energy of binding in protein interactions) Harvard (USA)
- ASPD (Artificial Selected Proteins/Peptides Database) Novosibirsk (Russian)
- ATID (alternative translational initiation database) Beijing (China)
- BBID (Biological Biochemical Image Database) NIA (USA)
- BIND (Biomolecular Interaction Network Database) VTO (Canada)
- BRENDA (Comprehensive Enzyme Information System) Cologne (Germany)
- BRITE (Biomolecular Relations in Information Transmission and Expression) GenomeNet (Japan)
- CellCircuits (a database of protein network models) California (USA)
- CheBI (dictionary of 'small molecular entities') EBI (UK)
- Chemical with Pharmaceutical Activity (3D database) Oxford (UK)
- CleanEx (a database of heterogeneous gene expression data based on a consistent gene nomenclature) Lausanne (Switzerland)
- CoC (a database of universally conserved residues in protein folds) MIT (USA)
- Complex Carbohydrate Structure Database CarbBank, voir aussi Search
- CutDB (a proteolytic event database) California (USA)
- Dasty (for visualising protein sequence feature information) EBI (UK)
- Defensins (a manually curated database and information source focused on the defensins family of antimicrobial peptides) Singapore
- Delta Mass (Database of Protein Post Translational Modifications) ABRF (USA)
- DSDBASE (database on disulphide bonds in proteins) Bangalore (India)
- DynaProt 2D (an advanced proteomic database for dynamic online access to proteomes and two-dimensional electrophoresis gels) TUM (Germany)
- EROP-Moscow oligopeptide database Moscow (Russian)
- EzCatDB (the Enzyme Catalytic-mechanism Database) Tokyo (Japan)
- Genes & proteins synonyms GPSDB (USA)
- Genes Networks Data Base (GeNet) Russian Network
- Gene Ontolgy Annotation (GOA) EBI (UK)
- GlycoMapsDB (database of the accessible conformational space of glycosidic linkages) Heidelberg (Germany)
- GlycoSuiteDB (relational database of glycan structures) GSDB (USA)
- GOBASE (Organelle Genome Database) Montreal
- GTOP (Genomes TO Protein structures and functions) NIG (Japan)
- HaptenDB (a comprehensive database of haptens, carrier proteins and anti-hapten antibodies) Chandigarh (India)
- HCNet (a database of heart and calcium functional network) Gwangju (Korea)
- InstaSeq (a Google powered bioinformatics search tool) Georgetown (USA)
- Intein Database BioLabs
- IntEnz (Integrated relational Enzyme database) EBI (UK)
- MAPU (Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes) Martinsried (Germany)
- mitBASE (a comprehensive and integrated mitochondrial genome database) SRS - EBI (UK)
- MITOCHONDRIOME (mitochondrial data and databases) Bari (Italy)
- MITOP (Database for mitochondria-related genes, proteins and diseases) MIPS (Germany), see also Mitop2
- MitoProteome (mitochondrial protein sequence database and annotation system) California (USA)
- Lipidat OSU, another link (USA)
- MACiE (a database of enzyme reaction mechanisms) Cambridge (UK)
- MetaRouter (bioinformatics for bioremediation) Madrid (Spain)
- OGRe (a relational database for comparative analysis of mitochondrial genomes) Manchester (UK), another link
- OPM (orientations of proteins in membranes database) Michigan (USA)
- ORegAnno (an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation) Vancouver (Canada)
- PeptideAtlas (compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments) Lausanne (Switzerland)
- PPD (database of experimentally determined protein pKa values) Berkshire (UK)
- Predictome (visualizing the predicted functional associations among genes and proteins) Boston (USA), another link
- ProNIT (Thermodynamic Database for Protein-Nucleic Acid Interactions) Kyushu (Japan)
- Protein Classification Benchmark collection for machine learning Trieste (Italy)
- Protein Folding Database Victoria (Australia)
- ProTherm (Thermodynamic Database for Proteins and Mutants) Kyushu (Japan)
- REFOLD database (a tool for the optimization of protein expression and refolding) Victoria (Australia)
- SELEX DB (high affinity DNA and RNA sequences) EMBNet (Russian)
- Seq2Struct (a resource for establishing sequence-structure links : Swiss-Prot + TrEMBL and PDB + SCOP) Rome (Italy)
- SPD (database of secreted protein database) Beijing (China)
- SuperDrug (a conformational drug database) Berlin (Germany)
- SuperHapten (a comprehensive database for small immunogenic compounds) Berlin (Germany)
- TAMAL (an integrated approach to choosing SNPs for genetic studies of human complex traits) North Carolina (USA)
- TAR-GET (identification of classes of proteins of biotechnological and pharmaceutical interest) ANL (USA)
- World-2DPage Expasy
- Alert : new sequences
- Sequence submission
- ADIT Validation Server (PDB) Rutgers (USA)
- BankIt sequence submission to GenBank (NCBI), see also Sequin (aid in the submission of sequences to the GenBank, EMBL, and DDBJ sequence databases)
- The EBI Sequence Data Submission WebIn, see the instructions (EMBL Database)
- The EBI Sequence Data Submission SwissProt
- SPIN (web-based tool for submitting directly sequenced protein sequences) EBI
- Information on submission of sequence data to the SWISS-PROT Data Bank Expasy (Switzerland)
- Informations on sequence submission EBI (EMBL)
- VERIFY3D Structure Submission UCLA-DOE
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