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Cn3D v4.1

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Taxonomy in MMDB


Research topics and staff

The NCBI Structure Group

.. maintains MMDB, a database of macromolecular 3D structures, as well as tools for their visualization and comparative analysis. MMDB, the Molecular Modeling Database, contains experimentally determined biopolymer structures obtained from the Protein Data Bank (PDB).

Structure highlights
Semi-automated annotation of taxonomic sources in MMDB has resulted in taxonomy links for about 38.000 molecules with 3D structure information. This allows for organism-based queries in Entrez's structure division. More..

Text searches in MMDB (use the search toolbar at the top of this page) will yield Structure Query pages, providing access to entries that matched the keywords. Structure Summary pages for one/several/all of these may be retrieved. From the Structure Summary pages one may:

  • access amino acid and nucleic acid sequences
  • retrieve PubMed documents
  • get taxonomy information
  • view sequence neighbors
  • view structure neighbors

try also:

Structure summary
via PDB/MMDB-Id:

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MMDB's FTP-site (including the MMDB database)

NCBI C++ Toolkit containing Cn3D source code.

Publications in Entrez

Research software: PKB and Threading (requires Splus).

Updated 07/07/04

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