Belozersky Institute


Russian EMBnet Node

Molecular Biology Databases

a) General

Protein sequences:

  • SwissProt
  • TREMBL : CDS features from EMBL as translated peptide sequences.
  • PIR
  • OWL : non-redundant database assembled from a number of primary sources including translations of nucleic acid sequences (Swissprot, PIR, NRL3-D and GenPept).

Nucleic acid sequences:

Three-dimensional structures:


b) Specialized

ProSite Functional protein sites
PRINTS Protein fingerprint database
BLOCKS Multiply aligned ungapped segments of proteins represented in the Prosite databank
SCOP, CATH Protein structural classifications
MMDB Molecular Modelling Database (NCBI, USA)
3DEE Database of Domain Definitions
FSSP PDB subset: families of Structurally Similar Proteins (EMBL)
Pfam Database of protein families and HMMs (collection of multiple sequence alignments and hidden Markov models)
PRODOM  Collection of protein families constructed by clustering all complete protein sequences in SwissProt.
PROTFAM Protein families constructed by clustering of protein sequences in PIR.
TGDB Tumor Gene Database: oncogenes and relevant genes
OMIM Online Mendelian Inheritance in Man: catalog of human genes and genetic disorders
GSDB The Genome Sequence Database: complete relational database of DNA sequences and annotation
GDB Genome Data Base
dbSNP Database of Single Nucleotide Polymorphisms
TIGR Database Genomes: human, Arabidopsis thaliana, Haemophilus influenzae, Mycoplasma genitalium
Saccharomyces Genome Database  
Candida albicans data  
Malaria Database  
FlyBase Drosophila database
The Mouse Genome Database  
ARS Genome Database Resource (USA) Genomes of cereals (wheat, rice, etc.), trees (apple, pine), and models (caenorhabditis, arabidopsis, etc.)
Animal Genome Database (Japan)  
Parasite Genome (EBI) Apicomplexa (incl. Plasmodium), Schistosoma, Tripanosoma, Leishmania, and Nematode DNA
ICTVdB A Universal Virus Database
HIV sequence Database (Los Alamos)  
EcoCyc Encyclopedia of Escherichia coli genes and metabolism, graphical user interface
NRSub Non-redundant database for Bacillus subtilis
YPD, WormPD Databases for proteins of Saccharomyces cerevisiae and Caenorhabditis elegans
TRRD Transcription Regulatory Regions Database (Eukaryotic genomes)
tRNA sequences  
rRNA WWW server (Antwerpen) Databases of ribosomal RNA
MITOMAP Human mitochondrial genome database
Histone Sequence Database  
KabatMan Database of antibody structure and sequence information
REBASE Database of restriction enzymes and methylases
LIGAND Ligand Chemical Database for Enzyme Reaction
MassBank Mass spectra of proteins
SWISS-2DPAGE Database of two-dimensional polyacrylamide gel electrophoresis
IMGT International ImMunoGeneTics database

DBCat (catalogue of databases)

A well-commented list of databases is contained also in DEAMBULUM