Workshop I

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 Session I Exercises



Entrez 3D Domain Help
   Entrez Searching: Entrez 3D Domains

Launch guide window Launch NCBI Home Page

Goals

  • Find 3D domain records using Entrez 3D Domains
  • Construct advanced queries using Preview/Index

Steps

  1. Begin with Preview/Index in Entrez 3D Domains
    • From the NCBI home page, click on the Domains & Structures category on the left side of the page.
    • Click on 3D Domains under Databases.
    • Click on Preview/Index to view the list of available fields.

  2. Search 1
    Find all structures of mammalian proteins containing only 2 helices and 2 strands. Use the fields [organism],[helixcount] and [strandcount], and add 'AND 0[domainno]' to limit to full protein chains (rather than internal 3D domains).

  3. Answer 1
    Click here to check your answer.

  4. Search 2
    Find all protein structures from green plants with molecular weights greater than 100 kDa. Use a term such as 100000:1000000[molweight].

  5. Answer 2
    Click here to check your answer.

  6. Search 3
    Find all polypeptide chains containing between 10 and 20 3D domains. First use the [domainno] field and the range operator ":". Example: 5:8[domainno] gives 5-8 3D domains. Find the polypeptide with the largest number of 3D domains. How many does it have?

  7. Answer 3
    Click here to check your answer.

  8. Search 4
    Find all human 3D Domains deposited to PDB between October 15, 2004 and November 15, 2004. Use the [PDB Deposit Date] field with date format YYYY/MM/DD.

  9. Answer 4
    Click here to check your answer.

Revised March 12, 2010