Lesson 1 -- How to do the protein data bank search

Objective: The PDB search GUI can do the protein search task to the PDB website. The PDB data is mirrored from the RCSB (www.rcsb.org) database.

Prerequisite: For PDB search, the target input and internet connection to PDB are needed. 

Procedure: In the protein data bank GUI, enter the following information in the appropriate place:

1. First click the button “ DB Client” on the CSE Online
2. Click the button “ Public Databases”. There appear one button “ Protein Databank ” and then click the button “ Protein Databank ”,you can see one new searching interface
3. The PDB search can by six methods: PDB id, Title, Author, Functional class, Source and Sequence. Select one search method from the “ field ” section
4. Select one operator from the “ Operator ” section (HAS or EQUALS)
5. Input your search target in the “ Value ” section. Then click the “ Execute Search ” button
6. There is your search results in the “ Results ” section
7. You can refine your search results by click the “ Add Refinement ” button. The input as the new search section. In the “ search using condition ” section you can select “ and ” or “ or ” do the search refinement
8. When the search is done, you can select one PDB file from the “ Results ” section. Click the “ View Details ” button to view the detail information of this PDB file or click “ Bioviewer ” button to view the structure of this PDB file

   new search interface

  refinement search interface

search results interface