Séquences
English version
Cette page vous présente quelques adresses de serveurs que vous pouvez interroger :
- Banques (Banques, Multi-banques)
- Banques de structures (BMRB, PDB, NRL ..)
- Nucléiques spécialisées (Usage codons, Vecteurs, Tags, Transcription, Promoteurs, ARN ..)
- Protéiques spécialisées (Motifs, Alignements, Domaines, Familles, Organes, Pathologie)
- Divers (Banques, utilitaires ..)
- EMBL, Genbank, NRSub, SwissProt, PIR, PDB, OWL, PMD, TREMBL, GBNew, EMNew, etc... avec liens :
Système SRS manuel : V.5,, V.7
Consulter périodiquement la liste des serveurs, banques et librairies
- SRS5
- EMBL, Heidelberg, Germany, - Data Banks
- Expasy, Geneva, Switzerland, - Data Banks
- IUBio, Indiana, USA, - Data Banks
- IVR, Kyoto, Japan, - Data Banks
- SRS6 ou SRS7 (*) ou 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 etc...
- 3DinSight (PDB, EMBL, Swiss-Prot, Mutant, Pir ..) Riken (Search Tool for Structure, Function and Property of Biomolecules) (Japon)
- 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 (Suisse)
- 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 lien avec Medline) www, voir aussi 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), voir aussi Expasy, ou encore PIR
- EMBL
- GenomeNet (Japon) www (DBGET)
- E.B.I (Cambridge) www
- SRS : sur tous les serveurs [SRS], disponible aussi EMNEW
- EXProt (database for EXPerimentally verified Protein functions)
- GenBank
- GenomeNet (Japon) www (DBGET)
- NCBI www, Inherited Disease Genes Identified by Positional Cloning, voir aussi Genome Survey Sequence dbGSS, voir aussi HTGS
- XPRO (database of eukaryotic protein-encoding DNA sequences in GenBank) NUS (Singapore)
- SRS : presque tous les serveurs [SRS], sauf EBI, Sanger
- Gene Ontology
- FatiGO - Data mining with Gene Ontology Valence (Espagne)
- 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 (Australie)
- 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 : miroir (incomplet) 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 : à EMBL-EBI (Angleterre)
- Kabat Sequence Database
- Mutations
- Cystic Fibrosis Mutation Data Base Toronto (Canada)
- Mutation Database Web server Melbourne (Australie), voir aussi l'EBI (UK)
- PMD (Protein Mutants Database) EMBL (Heidelberg), voir aussi Osaka (Japon), voir aussi NIG (Japon)
- OWL (Banque protéique non redondante)
- OWL (London) www
- Database Browser (OWL, PRINTS, ALIGN, GPCR, CATH, PDBsum) UCL (UK)
- Database Information Retriever (OWL, PRINTS) Manchester (UK)
- SRS : 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 : sur tous les serveurs [SRS]
- REPBASE
- SRS : (linked libraries : REPBASE) : EBI
- SwissProt
- AllAllDB CBRG (Suisse)
- GenomeNet (Japon) www (DBGET)
- E.B.I (Cambridge) www
- Expasy www : recherche par description, numéro d'accès, auteur, journal, texte, voir aussi documents de nomenclature et 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 (Allemagne)
- Taxonomy browser (Newt) EBI (UK)
- SRS : sur tous les serveurs [SRS], disponible aussi SWISSNEW
- SYFPEITHI
- Database of MHC ligands and peptide motifs Tuebingen (Allemagne)
- TREMBL (CDS features from EMBL as translated peptide sequences)
- SRS : PBIL (France), EBI (UK) disponible aussi 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) : liens 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 (France)
- 3DinSight Riken (Search Tool for Structure, Function and Property of Biomolecules) (Japon)
- 3DB Browser
- OCA
- Brookhaven RCSB
- Brookhaven : miroir à l'EBI, ICM (Pologne), 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 (Allemagne)
- Antibody Structures in the Protein Databank Whiteknights (UK)
- CSS (analysis of carbohydrate 3D structures derived from the PDB) Heidelberg (Allemagne)
- BSM (UK) Enzyme Structures Database www (Sous-ensemble)
- Dali database Helsinki (Finlande)
- Database of Structural Motifs in Proteins CDFD (Inde)
- DisProt (a database of protein disorder) Indiana (USA)
- PDBSite (database of the 3D structure of protein functional sites) Novosibirsk (Russie)
- EBI (Cambridge) SRS (liens HSSP, DSSP et FSSP)
- eF-site and PDBjViewer (database and viewer for protein functional sites) Yokohama (Japon)
- EMBL (Heidelberg) SRS
- EMBL liens avec HSSP (SRS)
- Fetch a PDB entry Pasteur (France)
- FireDB (a database of functionally important residues from proteins of known structure) Madrid (Espagne)
- 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) Londres (UK)
- HIC-Up (hetero-compounds encountered in PDB) Uppsala (Suède)
- 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 Londres (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 ou encore "at a glance" (classification fonction, organisme ..)
- 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 (Italie)
- PISCE (recent improvements to a PDB sequence culling server) Philadelphia (USA)
- ProMode (database of normal mode analysis of proteins) Tokyo (Japon)
- ProSAT (Protein Structure Annotation Tool) Heidelberg (Allemagne)
- 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 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 RELIBase
- Structural data about receptor/ligand complexes EBI (UK) (nécessite "Java viewer" et "VRML Helper")
- Structure SESAM
- A database for protein structures UCMB (Belgique)
- Structure SLoop
- Database of Super Secondary Fragments Cambridge (UK)
- Usage des codons
- Vecteurs - Oligo
- PlasmID (a centralized repository for plasmid clone information and distribution) Cambridge (USA)
- VectorDB (Phages, plasmids, cosmids, virus, YAC ...) Stanford (USA)
- SRS - VECTOR : BEN, (Belgique)
- Tags
- Mendel-ESTS MBG (UK)
- Séquences exprimées (dbEST - NCBI) www miroir à EBI
- Sites (dbSTS - NCBI) www miroir à EBI
- STACK (Sequence Tag Alignment and Consensus Knowledgebase) SANBI (Afrique du Sud)
- 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) : CSC (Finland) (+ DBSTS, DBSTSNEW), WEHI (Australie)
- Promoteurs eucaryotes
- EPD Database ISREC (Suisse)
- SRS (linked libraries : EPD) : sur tous les serveurs [SRS]
- Facteur de transcription - traduction
- RNA
- 5'-UTR and 3'-UTR of eukaryotic mRNAs Bari (Italie)
- 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 (Pologne)
- Database of ribosomal crosslinks Berlin (Allemagne)
- Databases of small and large ribosomal subunit RNA sequences (European ribosomal RNA database) Gent (Belgique)
- dbRES (database for annotated RNA editing sites) Beijing (Chine)
- EID (Exon-Intron Database) Ohio (USA)
- fRNAdb (a platform for mining/annotating functional RNA candidates from non-coding RNA sequences) Tokyo (Japon)
- 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 (France)
- Intron- Exon Knowledge Base Singapour, voir aussi Exint
- Intron Sequence and Information database Isis, autre lien (USA)
- Intron statistics Trieste (Italie)
- MeRNA (a database of metal ion binding sites in RNA structures) Berkeley (USA)
- MIDB (Eukaryotic Mismatched Intron Database) NUS (Singapour)
- 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 (Pologne)
- NATsDB (Natural Antisense Transcripts DataBase) Beijing (Chine)
- ncRNAdb (non coding RNAs database) Poznan (Pologne)
- Non-Canonical Base Pair Database Houston (USA)
- Noncoding RNAs Database Poznan (Pologne)
- ncRNA (RNAdb : a comprehensive mammalian noncoding RNA database) Queensland (Australie)
- NONCODE (an integrated knowledge database of non-coding RNAs) Beijing (Chine)
- NPIDB (database of Nucleic Acids-Protein Interactions) Moscou (Russie)
- NPInter (the noncoding RNAs and protein related biomacromolecules interaction database) Beijing (Chine)
- PACdb (PolyA Cleavage Site and 3'-UTR Database) Jackson (USA), voir aussi AtPACdb (for Arabidopsis thaliana)
- probeBase (resource for rRNA-targeted oligonucleotide probes) Vienne (Autriche)
- 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 (Japon)
- REDIdb (the RNA editing database) Calabria (Italie)
- Rfam (non-coding RNA families) Sanger (UK), voir aussi 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
- RNA Structure Database Rnabase (USA)
- 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 (Russie)
- 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 (France)
- Sno/scaRNAbase (a curated database for small nucleolar RNAs and cajal body-specific RNAs) Shanghai (Chine)
- SRPDB (Signal Recognition Particle Database) UTHCT
- SSU rRNA Modification Database Utah (USA)
- tmRNA database (earlier called "10S RNA")) UTHCT, voir aussi Indiana (USA), voir aussi Aarhus (Danemark)
- 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) Barcelone (Espagne)
- Sites spécifiques
- S/MARt DB (S/MAR transaction DataBase) Goettingen (Allemagne)
- TassDB (a database of alternative tandem splice sites) Freiburg (Allemagne)
- Autres
- ACUTS (Compilation of Ancient Conserved UnTranslated Sequences) ACNUC (Lyon)
- DDBJ (DNA Data Bank of Japan) NIG (Japon)
- 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 (France)
- Motifs protéiques, sites, alignements
- Alignements (famille de protéines)
- 3D_Ali (A database of aligned protein structures and related sequences) EMBL (Allemagne)
- CAMPASS (CAMbridge database of Protein Alignments organised as Structural Superfamilies) Cambridge (UK), voir aussi NCBS (Inde), voir aussi 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), autre lien
- MulPSSM (a database of multiple position-specific scoring matrices of protein domain families) Bangalore (Inde)
- PALI (Phylogeny and ALIgnment of homologous protein structures) CSBG (Inde)
- Phylogeny of the Unicellular Organisms Metabolic Pathways Alignments WIT (Argonne) (interconnexion voies métaboliques, séquences, alignements, phylogénie)
- ProtBuD (a database of biological unit structures of protein families and superfamilies) Philadelphia (USA)
- SIMAP (the similarity matrix of proteins) MIPS (Allemagne)
- 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) : voir les serveurs [SRS]
- BLOCKS
- Hutchinson Cancer Research Center www, miroir au Weizmann Institute
- SRS (linked libraries : BLOCKS) : voir les serveurs [SRS]
- CoPS (Comprehensive Peptide Signature Database) Delhi (Inde)
- HSSP (homology-derived structures of proteins)
- EBI
- SRS (libraries with protein structure information : HSSP) : EBI
- Interactions
- 3did (interacting protein domains of known three-dimensional structure) EMBL (Allemagne)
- AANT (Amino Acid-Nucleotide Interaction Database) Texas (USA)
- ABAC Database (equivalent binding sites reveal convergently evolved interaction motifs) Dresde (Allemagne)
- Adan (protein-protein interaction of modular domains) EMBL (Allemagne)
- 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 (Italie)
- 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 (Inde)
- 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 (Italie)
- MPPI (Mammalian Protein-Protein Interaction Database) MIPS (Allemagne)
- NPInter (the noncoding RNAs and protein related biomacromolecules interaction database) Beijing (Chine)
- 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 (Japon)
- PRECISE (database of Predicted and Consensus Interaction Sites in Enzymes) Boston (USA)
- Prodistin (functional classification of proteins based on interactions) Marseille (France)
- Protein-Protein Interaction Jena (Allemagne)
- PSIMAP (database of protein structural interactome map) Daejeon (Corée), autre lien
- 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 (Ecosse)
- STRING (known and predicted protein-protein associations, integrated and transferred across organisms) EMBL (Allemagne)
- UniHI (an entry gate to the human protein interactome) Berlin (Allemagne)
- MotifDic
- Search MotifDic database using DBGET (Prosite, Blocks, Prints, Prodom, Pfam) Kyoto (Japon)
- ProClass Database
- Prosite
- GenomeNet (Japon) www (DBGET)
- E.B.I (Interpro) www
- Expasy www
- SRS (linked libraries : PROSITE) : sur tous les serveurs [SRS], disponible aussi PROSITEDOC (dictionnaire)
- Protein Motif Fingerprint Database
- Domaines
- ADDA (a domain database with global coverage of the protein universe) Helsinki (Finlande)
- ArchDB (compilation of structural classifications of loops extracted from known protein structures) Barcelone (Espagne)
- 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, voir aussi Entrez (USA)
- COGs (Clusters of Orthologous Groups NCBI (USA)
- DIAL (automatic identification of structural domains in proteins) Tamilnadu (Inde)
- 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 (Suisse)
- InterPro (Integrated Resource of Protein Domain and Functional Sites) EBI (UK)
- PDBSite (database of the 3D structure of protein functional sites) Novosibirsk (Russie)
- 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 (Inde)
- PROF_ PAT 1.3 (Updated database of patterns used to detect local similarities) ICG (Russie)
- PRODOM
- PRODOM Toulouse (France)
- SRS (linked libraries : PRODOM) sur des serveurs [SRS]
- 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 (Allemagne)
- SURFACE (database of protein surface patches, defined as putative surface functional sites) Rome (Italie)
- Familles de protéines - gènes
- 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, voir aussi Washington, voir aussi Karolinska, voir aussi INRA
- Pfam : FunShift (database of function shift analysis on protein subfamilies) Stockholm (Suède)
- 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 (Autriche)
- ABC-transporter genes (human) Wageningen (The Netherlands)
- ABC transporter (Arabidopsis) TAIR (USA)
- ABCISSE (ATP Binding Cassette) Pasteur (France)
- ADME-AP (Drug ADME associated proteins) Singapour
- 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 (Pologne)
- Androgen receptor gene mutations database Montreal (Canada)
- ANTIMIC (a database of antimicrobial sequences) IIR (Singapore)
- AntiMicrobial Sequences Database AMSdb (Italie)
- 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) Rome (Italie)
- ATPase database (P-type) Copenhagen (Danemark)
- 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 (Russie)
- Conopeptide sequences and structures Queensland (Australie)
- CREMOFAC (database of chromatin remodeling factors) Bangalore (Inde)
- CSD (database for Cold Shock Domain) Marburg (Allemagne)
- Cytochrome P-450 (ICGEB Trieste) www, miroir à Budapest
- Cytochrome P450 2E1 UCHSC (USA)
- Cytokine Family cDNA Database Kumamoto (Japon)
- Cytokines Online Pathfinder Encyclopaedia COPE (Allemagne)
- 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 (Allemagne)
- ERGDB (Estrogen Responsive Genes Database) KELIIR (Singapore)
- Erythropoiesis database (EpoDB) CBIL (USA)
- eSLDB (eukaryotic subcellular localization database) Bologne (Italie)
- ESTerase and a/b Hydrolase Relatives (CHEDB) : superfamily of alpha/beta hydrolase which are homologous to cholinesterases INRA (Montpellier), autre lien
- Estrogen receptor resource Georgetown (USA)
- Expansin PennState (USA)
- EyeSite (a semi-automated database of protein families in the eye) Birbeck (UK)
- Facteur VIII HAMSTeRS (UK)
- FAD-dependent pyridine nucleotide oxidoreductases ICGEB (Italie)
- Flavodoxins ICGEB (Italie)
- FYVE finger proteins Bergen (Norvège)
- GeneNet (groups of coordinately working genes) Novosibirsk (Russie)
- GLIDA (GPCR-ligand database for chemical genomic drug discovery) Kyoto (Japon)
- Globines (Pennsylvania State University) www
- Glucocorticoid Receptor Resource Georgetown (USA)
- Glucose-6-Phosphate Dehydrogenase (G6PD) deficiency G6PD (USA), voir aussi 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) Moscou (Russie)
- Hera (human endoplasmic reticulum resident proteins database) Montreal (Canada)
- Histone Sequence Database NHGRI-NCBI (USA)
- Homeodomain Resource NHGRI (USA)
- HOX database IEPHB, voir aussi 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) (Allemagne)
- 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 : à EMBL-EBI (Angleterre)
- JenPep (peptides binding to MHC class I, II and TAP molecules) EJIVR (UK)
- Protéines kinase (PKR) SDSC (USA), voir aussi Sugen
- KSD (Kinase Sequence Database) UCSF (USA)
- Kinesin (mechanochemical protein) FHCRC
- KinG (database of protein kinases in genomes) Bangalore (Inde)
- KNOTTIN (knottins or inhibitor cystine knots, small disulfide-rich proteins with a knotted topology) CBS (France)
- L1CAM (Neuronal cell adhesion molecule : domains, mutations, sequences) Groningen (The Netherlands)
- Ligand-Gated Ion Channels database (manually curated) EBI (UK)
- Lipase Engineering Database Stuttgart (Allemagne)
- LOCATE (a mouse protein subcellular localization database) Queensland (Australie)
- LOX-DB (lipoxygenases database) Heidelberg (Allemagne)
- LOChom (database of predicted subcellular localization based on sequence homology) Columbia (USA), voir aussi 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 (Suisse), voir aussi index of MT Expasy
- MHC binding peptides WEHI (Australie)
- 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 (France)
- MitoDat : Mendelian Inheritance and the Mitochondrion database NCI
- Muscle-Specific Regulation of Transcription (MTIR) CBIL (USA)
- MutS TIGR (USA)
- Myosin MRC-LMB (UK), miroir à ProWeb
- NESbase (proteins in which the presence of Leucine-rich nuclear export signal (NES) has been experimentally verified) CBS (Danemark)
- 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), autre lien
- 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 (France)
- NURSA (hyperlinking the nuclear receptor signaling community) Texas (USA)
- O-glycosylated proteins database O-GlycBase (Danemark)
- Olfactory Receptor DataBase Yale
- Ovarian Kaleidoscope Database (OKDB) Stanford (USA)
- P53 (Structure, expression, modifications...) Curie (France)
- P53 mutations database Tokyo (Japon), voir aussi 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), voir aussi Prolysis (France)
- Peroxidase (plant) Genève (Suisse)
- Phenylalanine hydroxylase PAH (Canada)
- Phosphabase (phosphatases) Manchester (UK)
- Phosphodiesterase Washington (USA)
- Phosphoprotein Database (PPDB) NCI (USA)
- Phytochromes Jena (Allemagne)
- PIN (proteins interacting in nucleus) New York (USA)
- Plant-PI (plant protease inhibitor) Bari (Italie)
- PlasmaDB (Human Plasma Database) NCI (USA)
- PLPMDB (Pyridoxal-5'-phosphate dependent enzymes mutation database) Rome (Italie)
- 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, voir aussi Hits
- Protein Family TIGR (USA)
- Protein Family Cores Stanford (USA)
- Protéases et leurs inhibiteurs Prolysis (France)
- Récepteurs couplés aux protéines G NIH, voir aussi liste dans SwissProt, voir aussi "G P C R pattern recognition" UCL (UK), voir aussi 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 (Japon)
- Snake neurotoxin database Singapore
- SNP@Domain (resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences) Daejeon (Korea)
- SNF2 family of proteins TIGR (USA)
- STCDB (signal transduction classification) Bielefeld (Allemagne)
- Steroid Receptor Associated Proteins Resource Ohio (USA)
- SubLoc (database of protein subcellular localization) Beijing (Chine)
- SUPFAM (homologous families in Pfam and PALI) CSBG (Inde)
- SYSTERS (Protein Family Database) Max-Planck (Allemagne)
- 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 (Inde)
- TMPDB (transMembrane protein database) Hirosaki (Japon)
- Topoisomerase (Gyr b) ICB (Japon)
- TRAIT (transcripts expressed in human skeletal muscle) Padoue (Italie)
- 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 (Allemagne)
- TRRD (Transcription regulatory region) ICG (Russie)
- TSGDB (tumor suppressor gene database) Los Angeles (USA)
- UvrA (ABC (ATP binding cassette) superfamily of proteins) TIGR (USA)
- Venom composition Melbourne (Australie)
- Venom and toxin Melbourne (Australie)
- 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 (Belgique)
- Classification structurale des protéines
- 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 (Australie)
- Database Browser (OWL, PRINTS, ALIGN, GPCR, CATH, PDBsum) UCL (UK)
- DHS (dictionary of homologous superfamilies, built on CATH) Londres (UK)
- MinSet (a general approach to derive maximally representative database subsets by using fragment dictionaries and its application to the SCOP database) Londres (UK)
- QSCOP (SCOP quantified by structural relationships) Salzburg (Autriche)
- SCOP (Cambridge) www, voir aussi Berkeley, voir aussi Wehi
- SCOPPI (a structural classification of protein-protein interfaces) Dresden (Allemagne)
- Superfamily (Hidden Markov Models) Cambridge (UK)
- TOPS (an enhanced database of protein structural topology) Leeds (UK)
- Pathologie
- ALPSbase : Database of mutations causing human ALPS NHGRI-NIH (USA)
- Androgen Receptor Mutations Database Montréal (Canada)
- Angiogenesis related disease database Séoul (Republic of Korea)
- BCI Databases (Tumor, Breast cancer, Mamary transgene, GPCR list) BCI (USA), voir aussi BCF
- BIOMDB (Database of mutations causing tetrahydrobiopterin deficiencies) Zurich (Suisse)
- Breast Cancer Gene Database BCM (USA)
- BTKbase: Mutation registry for X-linked agammaglobulinemia Helsinki (Finlande)
- CD40L Defect Database (leads to X-linked Hyper-IgM syndrome) Expasy
- Connexin-deafness IRO (Espagne)
- CGAP (Cancer Genome Anatomy Project) NCI-NCBI (USA)
- DNA Patent Database DPD (USA)
- Fibrillin1 gene mutations implicated in Marfan Syndrome Necker (France)
- GENDIAG (Syndromes génétiques et développement : fusionné avec Orphanet) Paris (France)
- KinMutBase (disease-causing mutations in protein kinase domains) Helsinki (Finlande)
- LDLR gene in familial hypercholesterolemia UCL (England)
- OCRL1 Mutations Causing Lowe Syndrome NHGRI-NIH (USA)
- ORPHANET (base de données sur les maladies rares et les médicaments orphelins) Paris (France)
- PEDB (Prostate database) FHCRC (USA)
- PharmGED (pharmacogenetic effect database) Singapore
- TGD : Tumor Gene Database BCM (database of genes associated with tumorigenesis and cellular transformation)
- Divers
- AGML Central (web based gel proteomic infrastructure) South Carolina (USA)
- AliasServer (a web server to handle multiple aliases used to refer to proteins) Bordeaux (France)
- 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 (Belgique)
- 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 (Russie)
- ATID (alternative translational initiation database) Beijing (Chine)
- BBID (Biological Biochemical Image Database) NIA (USA)
- BIND (Biomolecular Interaction Network Database) VTO (Canada)
- BRENDA (Comprehensive Enzyme Information System) Cologne (Allemagne)
- BRITE (Biomolecular Relations in Information Transmission and Expression) GenomeNet (Japon)
- 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 (Suisse)
- 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 (Inde)
- DynaProt 2D (an advanced proteomic database for dynamic online access to proteomes and two-dimensional electrophoresis gels) TUM (Allemagne)
- EROP-Moscow oligopeptide database Moscou (Russie)
- EzCatDB (the Enzyme Catalytic-mechanism Database) Tokyo (Japon)
- 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 (Allemagne)
- GlycoSuiteDB (relational database of glycan structures) GSDB (USA)
- GOBASE (Organelle Genome Database) Montreal
- GTOP (Genomes TO Protein structures and functions) NIG (Japon)
- HaptenDB (a comprehensive database of haptens, carrier proteins and anti-hapten antibodies) Chandigarh (Inde)
- HCNet (a database of heart and calcium functional network) Gwangju (Corée)
- 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 (Allemagne)
- mitBASE (a comprehensive and integrated mitochondrial genome database) SRS - EBI (UK)
- MITOCHONDRIOME (mitochondrial data and databases) Bari (Italie)
- MITOP (Database for mitochondria-related genes, proteins and diseases) MIPS (Allemagne), voir aussi Mitop2
- MitoProteome (mitochondrial protein sequence database and annotation system) California (USA)
- Lipidat OSU, voir autre lien (USA)
- MACiE (a database of enzyme reaction mechanisms) Cambridge (UK)
- MetaRouter (bioinformatics for bioremediation) Madrid (Espagne)
- OGRe (a relational database for comparative analysis of mitochondrial genomes) Manchester (UK), autre lien
- 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 (Suisse)
- PPD (database of experimentally determined protein pKa values) Berkshire (UK)
- Predictome (visualizing the predicted functional associations among genes and proteins) Boston (USA), autre lien
- ProNIT (Thermodynamic Database for Protein-Nucleic Acid Interactions) Kyushu (Japon)
- Protein Classification Benchmark collection for machine learning Trieste (Italie)
- Protein Folding Database Victoria (Australie)
- ProTherm (Thermodynamic Database for Proteins and Mutants) Kyushu (Japon)
- REFOLD database (a tool for the optimization of protein expression and refolding) Victoria (Australie)
- SELEX DB (high affinity DNA and RNA sequences) EMBNet (Russie)
- Seq2Struct (a resource for establishing sequence-structure links : Swiss-Prot + TrEMBL and PDB + SCOP) Rome (Italie)
- SPD (database of secreted protein database) Beijing (Chine)
- SuperDrug (a conformational drug database) Berlin (Allemagne)
- SuperHapten (a comprehensive database for small immunogenic compounds) Berlin (Allemagne)
- 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
- Alerte : nouvelles séquences
- Swiss-Shop : Abonnement d'un an : Swiss-Prot entries (courrier une fois par semaine)
- Soumission de séquences
- ADIT Validation Server (PDB) Rutgers (USA)
- BankIt soumission d'une séquence à GenBank (NCBI), voir aussi Sequin (aid in the submission of sequences to the GenBank, EMBL, and DDBJ sequence databases)
- The EBI Sequence Data Submission WebIn lire les instructions (EMBL Database)
- The EBI Sequence Data Submission SwissProt
- SPIN (web-based tool for submitting directly sequenced protein sequences) EBI
- Information sur la soummission de séquences à SwissProt Expasy (Suisse)
- Informations sur la soumission EBI (EMBL)
- VERIFY3D Structure Submission UCLA-DOE
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