MMDB: Entrez's 3D-structure database

Nucleic Acids Res. 2003 Jan 1;31(1):474-7. doi: 10.1093/nar/gkg086.


Three-dimensional structures are now known within most protein families and it is likely, when searching a sequence database, that one will identify a homolog of known structure. The goal of Entrez's 3D-structure database is to make structure information and the functional annotation it can provide easily accessible to molecular biologists. To this end, Entrez's search engine provides several powerful features: (i) links between databases, for example between a protein's sequence and structure; (ii) pre-computed sequence and structure neighbors; and (iii) structure and sequence/structure alignment visualization. Here, we focus on a new feature of Entrez's Molecular Modeling Database (MMDB): Graphical summaries of the biological annotation available for each 3D structure, based on the results of automated comparative analysis. MMDB is available at:

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Computer Graphics
  • Databases, Protein*
  • Imaging, Three-Dimensional
  • Models, Molecular*
  • Protein Structure, Tertiary
  • Proteins / chemistry
  • Structural Homology, Protein*


  • Proteins