Workshop I

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 Session I Exercises



Entrez Structure Help
   Entrez Searching: Entrez Structure

Launch guide window Launch NCBI Home Page

Goals

  • Find structures using Entrez queries
  • Construct advanced queries using Preview/Index.

Steps

  1. Begin with Preview/Index in Entrez Structure
    • From the NCBI home page, click on the Domains & Structures category on the left side of the page.
    • Click on Structure under Databases.
    • Click on the Preview/Index tab near the top of the page to view the list of available fields.

  2. Search 1
    • All Entrez queries contain terms limited by fields and joined by Boolean operators, such as this query that retrieves all human 3D structures with exactly one protein chain:
      human[organism] AND 1[proteinchaincount]
    • Find all protein structures from primates. Use the fields [Organism] and [ProteinChainCount].
    • Add a term to your search to find all structures of protein-DNA complexes from primates containing only double-stranded DNA. Use the field [DnaChainCount].
    • Go to the next step to check your answer.

  3. Answer 1
    Click here to check your answer.

  4. Search 2
    • Using the [LigName] field, extend Search 1 to limit to only those complexes containing a zinc ion.
    • Go to the next step to check your answer.

  5. Answer 2
    Click here to check your answer.

  6. Search 3
    Find all complexes containing at least one protein chain, one DNA chain, and one RNA chain. First use "all[Filter]" to find all structures, then use terms such as "NOT 0[DnaChainCount]".

  7. Answer 3
    Click here to check your answer.

  8. Search 4
    • Find all structures determined by x-ray diffraction from Archaea at resolutions less than 2.0 Angstroms. Use the ":" range operator as follows: 0.0:2.0[resolution].
    • Use the [Filter] field to limit the results to those structures linked to SNP records, indicating that they are a structural model for a known SNP. Using Index in Preview/Index, look for terms in the [Filter] field such as "structure abc", which find links between structure and database abc.

  9. Answer 4
    Click here to check your answer.

  10. Search 5
    Find all fungal structures of single RNA chains only with one bound ligand.

  11. Answer 5
    Click here to check your answer.

Revised March 12, 2010