Worldwide Protein Data Bank (wwPDB)
  • wwPDB: The official wwPDB website
  • RCSB PDB: Research Collaboratory for Structural Bioinformatics PDB
  • PDBe: Protein Data Bank in Europe
  • PDBj: Protein Data Bank Japan
  • BMRB: Biological Magnetic Resonance Databank


  • ABG: Directory of 3D structures of antibodies
  • AfCS-Nature Signaling Gateway
    Comprehensive resource for information on cell signaling, including facts about the proteins involved in that process
  • BindingDB
    Database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.
  • BMCD
    Biological Macromolecule Crystallization
    The Comprehensive Enzyme Information System
  • CAZy
    Carbohydrate-Active enZYmes
  • CCDC
    Cambridge Crystallographic Data Centre (small molecules)
  • CoSSMos
    RNA Characterization of Secondary Structure Motifs (RNA CoSSMos) database. This tool allows the systematic searching of all catalogued three-dimensional nucleic acid PDB structures that contain secondary structure motifs such as mismatches, (a)symmetric internal loops, hairpin loops, and bulge loops.
  • Database of Macromolecular Movements
    Describes the motions that occur in proteins and other macromolecules, particularly using movies
  • DashPDB
    Mac OS X Dashboard widget that accesses PDB data files from RCSB PDB
  • EM DataBank
    The unified data resource for CryoEM
    Enzyme Nomenclature
  • Entrez
    NCBI databases
  • ExPASy
    Molecular Biology server
  • GeneCards
    Database on human genes, proteins and diseases
  • GenBank
    Nucleotide sequences
  • HIV Protease Database
  • Human Mitochondrial Protein Database
    Comprehensive data compiled from various resources on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function
  • IEDB
    The Immune Epitope Database contains data related to antibody and T cell epitopes for humans, non-human primates, rodents, and other animal species.
  • IMGT
    International ImMunoGeneTics Database
  • LS-SNP
    A web tool for genome-wide annotation of human SNPs. The current version, LS-SNP/PDB, provides information useful for identifying amino-acid changing SNPs (nsSNPs) that are most likely to have an impact on biological function.
  • Membrane Protein Data Bank
    A relational database with select structural and functional information on membrane proteins and peptides
    Peptidase Database
  • ModBase
    A database of comparative protein structure models
  • NDB
    Nucleic Acid Database
  • OCA
    A browser-database for structure/function
  • PDB at a Glance
    Classification of the structures in the PDB
  • PDBbind
    Collecting experimentally determined binding affinity data exclusively for all types of biomolecular complexes in the Protein Data Bank, including protein-small molecule, nucleic acid-small molecule, protein-protein, and protein-nucleic acid complexes.
  • PDBLite
    Simple PDB search for students and educators
  • Pfam
    The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models.
  • ProNIT
    Thermodynamic Database for Protein-Nucleic Acid Interactions
  • Proteopedia
    Collaborative 3D encyclopedia of proteins and other molecules
  • ProTherm
    Thermodynamic Database for Proteins and Mutants
  • RELIBase
    Structural data about receptor/ligand complexes
  • SWISS-MODEL Repository
    A database of annotated protein structure homology models
  • UniProtKB
    A comprehensive, high-quality, and freely accessible resource of protein sequence and functional information.
  • Vitamin D Nuclear Receptor Site
  • Zinc
    A free database of commercially-available compounds for virtual screening.

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