3D-GENOMICS, BioMolecular Modelling server
3D Disaccharide Database
3D Glycosyltransferase Database
3D Lectin database
3D Monosaccharide database
3D saccharide databases
3Dee, a Database of Protein Domain Definitions. Rather than call the Database of Domain Definitions, DDD, the name 3Dee was chosen to show the link with three-dimensional (3D) structures.
ArkDB, Animal Genome, Mapping databases with the ARK System, available for cat, cattle, cow, chicken, deer, horse, pig, sheep, tilapia, turkey.
BACTIBASE, a data repository of bacteriocin natural antimicrobial peptides
Bacterial Polysaccharide Gene Database (BPGD)
BAliBASE, a benchmark alignments database for the evaluation of multiple sequence alignment programs
BIND, Biomolecular Interaction Network Database
BioCatalog software at EBI European Bioinformatics Institute, a software directory of general interest in molecular biology and genetics.
BioMed Central Databases, a catalog of biomedical databases
Bio-mirror, a public service for high-speed access to up-to-date DNA and protein sequence databanks
Blood Group Antigen Mutation Database
CATH, Protein Structure Classification, provides a hierarchical domain classification of protein structures. There are four major levels in this hierarchy: Class, Architecture, Topology (fold family) and Homologous superfamily.
CEPH Genotype database, Centre d'Etude du Polymorphisme Humain, Fondation Jean Dausset, a database of genotypes for genetic markers.
ConoServer, a database for conopeptide sequences and structures
CSD, The Cambridge Structural Database, contains crystal structure information for organic and metal organic compounds.
Dali Database, Dali structural neighbours. The Dali Database is based on all-against-all 3D structure comparison of protein structures in the Protein Data Bank (PDB).
DBAASP - Database of Antimicrobial Activity and Structure of Peptides
dbCFC, Cytokine Family cDNA database, Kumamoto, Japan
dbEST, database of Expressed Sequence Tags, NCBI, USA
dbGSS, database of Genome Survey Sequences, NCBI, USA
dbPTM, an integrated resource for protein post-translational modifications (PTM).
dbSTS, database of Sequences Tagged Sites, NCBI, USA
DDBJ, DNA Data Bank of Japan
Dfam, database of repetitive DNA families (collection of DNA Transposable Element sequence alignments, hidden Markov Models (HMMs), consensus sequences, and genome annotations)
DIP, Database of Interacting Proteins
DOGS - Database Of Genome Sizes
Eco Cyc , Encyclopedia of E.Coli Genes and Metabolism. This project consists of compiling a large knowledge describing the genes and metabolic pathways of the bacterium E.Coli.
EMBL, Nucleotide sequence database, EBI, UK
Entrez (NCBI), allows to retrieve molecular biology data and bibliographic citations of several searchable database of nucleotides, proteins, 3-D structures, genomes, maintained by NCBI.
Entrez Gene, a searchable database of genes (NCBI)
ENZYME, Enzyme nomenclature database, SIB, Geneva, Switzerland
EPD, Eukaryotic Promoter Database
Escherichia coli O-antigen Database
FIDD, Frequency of Inherited Disorders Database, Cardiff University School of Medicine, UK
FishBase, a global information system on fishes.
Fish net, an access to Zebrafish Research Databases.
FlyBase, a database of biological and genetic information about Drosophila, Indiana University, USA
GenBank, NCBI, USA, the NIH database of nucleotide sequences
Gene Knockout Database, Gene knockouts listed alphabetically according to the name of the gene.
GeneCards, Weizmann Institute, Israël TM , an automatically generated database of human genes, their products and their involvement in diseases.
GeneNetWorks, database on gene network components.
HemoPDB, Hematopoiesis Promoter Database, The Wistar Institute, Ohio State University, USA
HGMD, the Human Gene Mutation Database, Cardiff, UK
HGVbase, Human Genome Variation database
HIV Databases, Los Alamos National Laboratory
Human Disease to Drosophila Gene Database, utilizes the sequence information of
human disease genes from the NCBI OMIM database in order to determine if
sequence homologs of these genes exist in the current Drosophila sequence
IARC TP53 database, TP53 gene mutations identified in human cancers
ICBS, Inter-Chain Beta-Sheets, a database of beta-sheet formation protein-protein interactions mediated by interchain
ICTV, International Committee on Taxonomy of Viruses
IMB Jena Image Library Database of Sites
IMB Jena Image Library of Biological Macromolecules
IMGT/3Dstructure-DB, gene and allele identification of immunoglobulins (IG), T cell receptor (TR) and MH with known 3D structure, Montpellier, France
IMGT/GENE-DB, database of human immunoglobulin (IG) and T cell receptor (TR) genes, Montpellier, France
IMGT/LIGM-DB, nucleotide sequence database of immunoglobulin (IG) and T cell receptor (TR), Montpellier, France
IMGT/mAb-DB, database of monoclonal antibodies (IG, mAb) and fusion proteins for immune applications (FPIA), Montpellier, France
IMGT/MHC-DB, sequence database, EBI, UK
IMGT/PRIMER-DB, database of oligonucleotides for immunoglobulins (IG) and T cell receptors (TR), Montpellier, France
Integbio.jp, Portal site for Life Science Database Integration, Japan
International Nucleotide Sequence Database Collaboration, NCBI
ISIS, Intron Sequence and Information database test system, a database of nuclear introns.
IUPHAR-DB, database of G Protein-Coupled Receptors, Voltage-Gated Ion Channels, Ligand-Gated Ion Channels and Nuclear Hormone Receptors.
IUBio Archive for Biology data and software, an archive of biology data and software in the field of molecular biology
KEGG, Kyoto Encyclopedia of Genes and Genomes, Kyoto, Japan
LIGAND, database of chemical compounds and reactions in biological pathways, Kyoto, Japan
MEROPS, The Peptidase Database
MetaBase, the database of biological databases!
MGD, Mouse Genome Database, The Jackson Laboratory, USA, a database about the genetics of mice, containing experimental mapping data, probes, PCR primers and polymorphisms
MIPS, Munich information center for protein sequences
MitoDat, mitochondrial nuclear genes.
MITOMAP, a human mitochondrial genome database.
Modules. The module pages contain information and research tools (SMART) on protein domains, 1D and 3D cartoons of modular extracellular and intracellular proteins.
Molecules To Go, search of PDB
NRL-3D, a database produced by PIR from sequence and annotation information extracted from three-dimensional structures in the PDB, Washington DC, USA
NuReBase, NUclear REceptor dataBASE, Lyon, France, a nuclear hormone receptor database
O-GLYCBASE, CBS, Center for Biological Sequence Analysis, Lyngby, Denmark, a revised database of O-glycosylated proteins, data available by anonymous ftp.
OMIA, Online Mendelian Inheritance in Animals, University of Sydney, Australia
OMIM, Online Mendelian Inheritance in Man, NCBI, USA Ortholog databases
EGO, Eukaryotic Gene Orthologues (formerly known as TOGA - TIGR Orthologous Gene Alignment), Ortholog database, Orthologs of Human Disease Genes
HomoloGene, a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes, at NCBI
InParanoid, Eukaryotic Ortholog Groups
OrthoMCL DB, Ortholog Groups of Protein Sequences
OWL a non-redundant proteine sequence database produced from SWISS-PROT, PIR, GenBank, NRL-3D.
PAZAR, A public database of transcription factors and regulation sequence annotation.
PDB, Protein Data Bank, Research Collaboratory for Structural Bioinformatics, USA, an archive of experimentally determined 3-D structures of biological molecules which contains atomic coordinates, crystallographic and NMR data.
PenBase, Penaeidin database, curated database of antimicrobial peptides from penaeid shrimps
Pfam, Protein families database of alignments and Hidden Markov Models (HMMs), at the Sanger Centre, a comprehensive collection of protein multiple sequence alignments.
PIR, Protein Information Resource, a division of the National Biomedical Research Foundation
( NBRF, USA), maintains the PIR-International Protein Sequence Database.
PKR, the Protein Kinase Resource, enzymology, genetics and molecular properties of protein kinases.
PlaNet, a network of European Plant Databases
PMD, Protein Mutant Database, a compilation of protein mutant data for all proteins except members of the globin and immunoglobulin families, based on literature.
PPDB, Phosphoprotein Database
PRINTS, Protein Motif Fingerprint Database, a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterize a protein family.
ProDom, The Protein Domain Database, Toulouse, France, consists of an automatic compilation of homologous domains.
PROSITE, SIB, Geneva, Switzerland, database of protein families and domains, detection of sequence patterns. Proteins families
Protein Data Bank in Europe : PDBe new service links (EBI)
PROW, Protein Rewiews on the Web (NCBI, USA), Editors: Stephen Shaw, Lisa A. Turni and Kenneth S. Katz, authoritative short structured reviews on proteins, protein families and CD molecules.
RATMAP, The Rat Genome Database
REBASE, The Restriction Enzyme Database, restriction enzymes and methylases.
ReLiBase, a program for searching protein-ligand databases.
RGD, Rat Genome Database
SCOP, Structural Classification of Proteins, Cambridge, UK
SGD, The Saccharomyces Genome Database
Short Tandem Repeat DNA Internet Database
smiRNAdb, human, mouse and rat small RNAs
SRPDB, Signal Recognition Particle Database
STD Sequence Databases, Los Alamos National Laboratory, molecular information on sexually transmitted bacteria and viruses.
SWISS-3DIMAGE, 3D images of proteins.
Swiss-Prot, SIB, Geneva, Switzerland, a curated database of protein sequences.
TAED, The Adaptive Evolution Database
Tandem repeats database - Minisatellite database, University Paris XI (Orsay), France
The KNOTTIN database, a database of knottins, proteins with knotted disulfide bridges, which include protease inhibitors, toxins, etc.
The Tumor Gene Family of Databases
TMbase, a database of TransMembrane proteins and their helical membrane-spanning domains.
TRANSFAC® - Gene Transcription Factor Database
TreeBASE, a Database of Phylogenetic Knowledge
TRIPS, a database of... Tandem Repeats in Protein Sequences.
UM-BBD, The University of Minnesota Biocatalysis/Biodegradation Database. This database contains information on microbial biocatalytic reactions and biodegradations pathways for primarily xenobiotic, chemical compounds.
UMD, Universal Mutation Database, Paris, France
UniGene, NCBI, USA
UniProt, a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.
Variation Databases and Related sites
Virus databases on-line
in the The IMGT Immunoinformatics page