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Belozersky Institute

GeneBee Service

Russian EMBnet Node

Molecular Biology Databases

Sequences

Uniprot Protein sequences
ENAGenBankDDBJ Nucleic acid sequences
rRNA European ribosomal RNA database
SILVA rRNA database

3-dimensional structures and derived information

Protein Data Bank (PDB) Proteins and other macromolecules
Nucleic Acid Database (NDB) Nucleic acids and their complexes
NCBI Structure Group
PDBe Protein Data Bank in Europe (EBI)
ProNIT Thermodynamic database for protein-nucleic acids interactions (Japan)
SCOPCATH Protein structural classifications
Dali database (FSSP) Families of structurally similar proteins

Homology families, multiple alignments

ProSite Functional protein sites
Pfam Database of protein families and HMMs (collection of multiple sequence alignments and hidden Markov models)
Rfam Database of RNA families and HMMs (collection of multiple sequence alignments and hidden Markov models)
PRINTS Protein fingerprint database
BLOCKS Multiply aligned ungapped segments of proteins represented in the Prosite databank
COGs Clusters of orthologous groups of proteins
PRODOM  Collection of protein families constructed by clustering complete protein sequences.

Genes and genomes

OMIM Online Mendelian Inheritance in Man: catalog of human genes and genetic disorders
Ensembl Genome Browser (complete animal genomes)
dbSNP Database of Single Nucleotide Polymorphisms
ICTVdB A Universal Virus Database
HERVd Human endogenous retrovirus database

Other

TRRD Transcription Regulatory Regions Database (Eukaryotic genomes)
MITOMAP Human mitochondrial genome database
Antibodies – Structure and Sequence  
REBASE Database of restriction enzymes and methylases
KEGG Kyoto Encyclopedia of Genes and Genomes
SWISS-2DPAGE Database of two-dimensional polyacrylamide gel electrophoresis

Database issues of NAR: vol. 31 (2003), vol. 32 (2004), vol. 33 (2005), vol. 34 (2006), vol. 35 (2007), vol. 36 (2008).