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Molecular Modeling DataBase

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 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.

URL: http://www.ncbi.nlm.nih.gov/structure

Resource ID: nlx_56387     Resource Type: Resource     Version: Latest Version


macromolecule, structure, 3d spatial image, protein structure, gold standard

Additional Resource Types




Resource Status

Last checked up;


MMDB, Structure


Entrez Structure, Structure database, NCBI Structure, Structure (Molecular Modeling Database)

Parent Organization

Curation Status


Alternate URLs


Resource PubMed IDs

PMID: 12967490, PMID: 19458762, PMID: 21359189, PMID: 21719536, PMID: 22135289, PMID: 22566848, PMID: 22639651, PMID: 23133621, PMID: 23505486, PMID: 23797979, PMID: 23915275, PMID: 24147010, PMID: 24319143, PMID: 24319143, PMID: 25138051, PMID: 25271995

Original Submitter


Version Status


Submitted On

12:00am April 13, 2011

Originated From


Changes from Previous Version

First Version

Version 1

Created 4 years ago by Anonymous