Bioinformatics Databases

Embase (often styled EMBASE for Excerpta Medica dataBASE) is a biomedical and pharmacological database of published literature designed to support information managers and pharmacovigilance in complying with the regulatory requirements of a licensed drug.

UniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects.

The Protein Data Bank (PDB) is a crystallographic database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids.

PROSITE is a protein database. It consists of entries describing the protein families, domains and functional sites as well as amino acid patterns and profiles in them.

The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine the evolutionary relationship between proteins.

DECIPHER is a web-based resource and database of genomic variation data from analysis of patient DNA. It documents submicroscopic chromosome abnormalities (microdeletions and duplications) and pathogenic sequence variants (single nucleotide variants - SNVs, Insertions, Deletions, InDels), from over 25000 patients and maps them to the human genome using Ensembl or UCSC Genome Browser.

The Biological Macromolecule Crystallization Database (BMCD) contains molecule, crystal and crystallization data for macromolecules for which diffraction quality crystals have been obtained. These include proteins and nucleic acids, various complexes, and viruses.

InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them.

CAZy is a database of Carbohydrate-Active enZYmes (CAZymes). The database contains a classification and associated information about enzymes involved in the synthesis, metabolism, and transport of carbohydrates.

The Biological General Repository for Interaction Datasets (BioGRID) is a curated biological database of protein-protein interactions, genetic interactions, chemical interactions, and post-translational modifications created in 2003 (originally referred to as simply the General Repository for Interaction Datasets (GRID) by Mike Tyers, Bobby-Joe Breitkreutz, and Chris Stark at the Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital.

BRENDA (BRaunschweig ENzyme DAtabase) is an enzyme information system representing one of the most comprehensive enzyme repositories.

MUMmer is a bioinformatics software system for sequence alignment. It is based on the suffix tree data structure and is one of the fastest and most efficient systems available for this task, enabling it to be applied to very long sequences.

SILVA is a comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data.

TRANSFAC (TRANScription FACtor database) is a manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. The contents of the database can be used to predict potential transcription factor binding sites.

Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank sequence database.