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How to retrieve 3D structures for a specific type of molecule, such as protein, RNA, or DNA

The "Retrieve 3D Structures that have..." buttons near the bottom of the 3D Macromolecular Structures page allow you to retrieve various molecule combinations (Protein+Chemical, RNA+Chemical, etc.) with a single click. If you prefer to construct those searches yourself, or to construct variations of those searches, this page shows you how.

  Method 1:   Search the Entrez Structure Database (MMDB) to retrieve 3D structure records that contain a desired number of DNA molecules, RNA molecules, protein molecules, and/or bound chemicals, using the Advanced Search page  
  1. Open the Entrez Structure Database (MMDB) search page.

  2. Select the "Advanced" option at the top of the page.

  3. On the Advanced Search Builder page, open the All Fields pull-down menu to see the available choices of search fields.

  4. The list of search fields includes:

  5. Molecule counts in the structure's biological unit:

    Molecule counts in the structure's asymmetric unit:

  6. Select the search field that represents the molecule count of interest, and in the query box beside the search field menu, enter the desired number of molecules that should be present in each retrieved structure record. You can enter an integer (e.g., 3) or a range (e.g., 1:999). Then press the "Search" button to retrieve the structures that contain the specified number of molecules (or click the "Add to history" link to list the search on the current page, along with the number of hits retrieved, and continue searching if desired).

    Additional tips:

    • To see the range of values available for a given molecule type, click on the "Show Index" link after selecting the desired field.
    • To retrieve all structure records that contain a specific molecule type, regardless of count, enter a value such as 1:999, where the colon serves as a range operator to retrieve records containing any number of molecules between the specified bounds.
    • To exclude a specific molecule type from retrieved structure records, enter a value of 0 (zero) beside the search field selection.

  7. If you are interested in several different molecule counts, you can do a separate search for each one. All of your searches will be be listed in the "History" section of the "Advanced Search Builder" page. You can then combine the searches using Boolean operators (AND, OR, NOT) or using the range search operator (:), as described in the search methods section of the main MMDB help document.

  Method 2:   Search the Entrez Structure Database (MMDB) by simply entering a complex Boolean search statement in the query box at the top of the page, then pressing the "Search" button. For example, to retrieve 3D structure records that contain proteins bound to ligands, but no DNA or RNA molecules, enter the following search:  
    1:999[ProteinMoleculeCount] AND 1:999[LigCount] AND 0[DNAMoleculeCount] AND 0[RNAMoleculeCount]

      The search methods section of the main MMDB help document provides additional tips about range searches and complex Boolean searches.  
  See Also:   Retrieve 3D structures bound to a specific chemical (e.g., aspirin)
Retrieve 3D structures bound to a specific small biopolymer (e.g., a peptide)

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