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Structure Database from NLM

Three dimensional structures provide a wealth of information on the biological function, on mechanisms linked to the function, and on the evolutionary history of and relationships between macromolecules. Most 3D-structure data are obtained from X-ray crystallography and NMR-spectroscopy.

The Molecular Modeling DataBase (MMDB), also known as "Entrez Structure," is a database of experimentally determined structures obtained from the RCSB Protein Data Bank (PDB). MMDB is developed by the Structure Group of the NCBI Computational Biology Branch. The data processing procedure at NCBI results in the addition of a number of useful features that facilitate computation on the data and link them to many other data types in the Entrez system. The help document and how to pages provides examples of how the database can be used.

The structure database is considerably smaller than Entrez's Protein or Nucleotide databases, but a large fraction of all known protein sequences have homologs in this set, and one may often learn more about a protein by examining 3-D structures of its homologs. These are accessible as "Related Structures" in the "Links" menu of Entrez Protein sequence records (illustrated example). It is then possible to align the query protein to the structure-based sequence, as shown in the illustration on this page.

Additional resources can be used along with MMDB to interactively view the structures, find similar 3D structures, learn about the types of interactions and bound chemicals that have been found to exist among the similar 3D structures, and more.


September 13, 2010


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