How To Use the Molecular Modeling Database (MMDB): search by molecule type

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3D Macromolecular Structures

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

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The "View 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, 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 chains, RNA chains, protein chains, and/or bound chemicals, using the Preview/Index page

Open the Entrez Structure Database (MMDB) search page.

Select the Preview/Index folder tab.

Open the All Fields pull-down menu to see the available choices of search fields.

The search field list includes:

DNAChainCount

ProteinChainCount

RNAChainCount

LigCount (short for "ligand" count, representing the number of chemicals bound to the structure).

Select the search field that represents the molecule of interest, and in the query box beside the search field menu, enter the desired number of chains 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 "AND" button to move that number and search field combination up to the active query text box at the top of the page.

To see the range of values available for a given molecule type, press the "Index" button after selecting the desired field.

To retrieve all structure records that contain a specific molecule type, regardless of chain count, enter a value such as 1:999, where the colon serves as a range operator to retrieve records containing any number of chains 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.

Repeat step 5 for each additional molecule type that you would like to have in the retrieved structure records.


	Method 2:		Search the 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 "Go" button. For example, to retrieve 3D structure records that contain proteins bound to ligands, but no DNA or RNA chains, enter the search:

			1:999[ProteinChainCount] AND 1:999[LigCount] AND 0[DNAChainCount] AND 0[RNAChainCount]


	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)

| Revised 10 September 2009 |