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The MMDB 3D structure database

MMDB (for Molecular Modeling DataBase) contains experimental data from crystallographic and NMR structure determinations. The data for MMDB are obtained from the Protein Data Bank (PDB). The NCBI has cross-linked structural data to bibliographic information, to the sequence databases, and to the NCBI taxonomy.

NCBI has developed a 3D structure viewer, Cn3D, for easy interactive visualization of molecular structures from Entrez.

MMDB structural data of proteins are compared against each other using the VAST algorithm for detecting significantly similar substructures. Entrez can be used to retrieve structures which seem highly similar to the query protein structure, in much the same way as sequence neighbors computed by BLAST. This will retrieve almost all structures with an identical 3-dimensional "fold", though it may occasionally miss a few or report chance similarities. The detection of structural similarity in the absence of obvious sequence similarity is a powerful tool to study remote homologies and protein evolution.

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