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Once a search is complete a table of PDB files relating to your search query will be displayed. To view the PDB file in 3D in the graphical display double click on a row in the PDBSearchResults table.

NOTE: If you have a PDB structure already saved you can read it into ICM by going to the File Menu and selecting Open. PDB files that have been viewed previously can be loaded using File/ Recent PDB Codes.

4.1.1 Searching the PDB

[ Keyword or PDB Code | Search PDB by Sequence | Search PDB by Ligand Code | Search by PDB Field ]

Protein structures solved by X-ray crystallography, NMR or other experimental methods are stored in the Protein Data Bank (PDB). These structures can be easily accessed, displayed and analyzed using ICM.

There are a number of different ways to find a structure from the PDB database and load it into ICM: You can query the PDB using the following options:

4.1.1.1 Query PDB by Keyword or PDB Code

Query by Keyword of PDB Code

• Click on the PDB search tab.
• Enter the PDB code or search string.
• Click on the search button to run the search.
• A list of related PDB entries based on your search will be displayed in the PDBSearchResults table of the graphical user interface.

Or

• Select Edit/PDB search and the "Find PDB Entries by Keyword" data entry window will be displayed.
• Enter a keyword or PDB code into the Keywords data entry field.
• Click the OK button and a list of related PDB entries based on your search will be displayed in the PDBSearchResults table of the graphical user interface.

NOTE: If a keyword has been entered previously it will be available by clicking on the drop-down button.

4.1.1.2 Query PDB by Sequence

To query the PDB by sequence:

• Click on the PDB search tab.
• Select the drop down arrow and select one of the following options

Seq Pattern- Enter a protein sequence and this option will tell you whether a protein structure exists in the PDB for that sequence.

Close Match- Enter a protein sequence and this option will tell you which sequences are similar to your entered sequence.

Homology- Enter a protein sequence and homologous proteins in the PDB will be displayed in a table.

• Click the Search button and a list of related PDB entries based on your search will be displayed in the PDBSearchResults table of the graphical user interface.

To query the PDB by ligand code:

• Click on the PDB search tab.
• Select the drop down arrow and select ligand code option from the list.
• Enter the ligand code and press the search button.
• Click the Search button and a list of related PDB entries based on your search will be displayed in the PDBSearchResults table of the graphical user interface.

4.1.1.4 Query PDB by PDB Field

To query the PDB by field (Author, Compound, PDB Header, Experiment Type, Resolution or Ligand Code

• Select Edit/PDB search by field.
• Enter the search string or value
• Click OK and a list of related PDB entries based on your search will be displayed in the PDBSearchResults table of the graphical user interface.

4.1.2 Sensitive PDB Similarity Searches

There are two ways to search a sequence against the PDB database.

OPTION 1:

If your sequence is already loaded into ICM:

• Select Edit/PDB Search by sensitive similarity
• Type the sequence name into the Sequence name field. Sequences which are already loaded into ICM can be seen by clicking the drop-down button
• Select the number of hits you wish to see by typing the number into the Limit field. A number can also be selected by clicking on the up and down arrows. (Default is 50)
• Select the sensitivity of your search by typing a value into the Expect field. This value is a database-size error estimate and the default value is 0.01.
• Choose whether you wish to display All entries or Entries with unique sequence by checking the appropriate button.
• If you wish to load the sequences leave the Load Sequences box checked.
• If you merely want to see the PDB codes which are similar to your sequence then un-check the Load Sequences box.
• Click the OK button.

OPTION 2:

If your PDB sequence is not loaded into ICM:

• Select Edit/Search with external sequence
• Cut and paste or type (shown below) your sequence into the Sequence data entry field.
• Select the number of hits you wish to see by typing the number into the Limit field. A number can also be selected by clicking on the up and down arrows. (Default is 50)
• Select the sensitivity of your search by typing a value into the Expect field. This value is a database-size error estimate and the default value is 0.01.
• Choose whether you wish to display All entries or ** Entries with unique sequence ** by checking the appropriate button.
• If you wish to load the sequences leave the Load Sequences box checked.

NOTE: If you merely want to see the PDB codes which are similar to your sequence then un-check the Load Sequences box.

• Click the OK button.

NOTE: You can also use the toolbar search option by homology if you wish.

4.1.3 PDB Search Results Table

Once you have searched for a PDB structure, a table with the search results will be displayed on the bottom of the ICM window. See the Tables section for more information on how to use ICM tables. See the next section loading your PDB file for information how to view the PDB file. More information about working with tables can be found in the Tables Section of this manual.

• To load a pdb file double click on the search results table.
• Sort the table by right clicking on the column header. Other table manipulation options are described in the Working with Tables chapter.

NOTE: In the table there are blue hyperlinks directing you to the PDB and Uniprot websites.

4.1.4 Loading Your PDB File

• To load a pdb file double click on the search results table.
• Sort the table by right clicking on the column header. Other table manipulatio n options are described in the Working with Tables chapter.

4.1.5 Load and Display NMR Structures

Use the PDB Search tab to load NMR structures from the PDB. You can use the drop down button shown below to determine how you want to display your NMR structure. You can choose to display and download the first NMR model, all models in the PDB file or all models in the PDB in a stack. If you choose the stack option the the stack will be stored in the object as described here.

4.1.6 Occupancy Display

You can use the options in the PDB Search tab to control if and how the partial or zero atom occupancies are displayed. You can choose to circle or label the poor occupancy atoms.

4.1.7 Hyperlinks to PDB Website and UniProt

In the PDB Search Results Table you will see blue hyperlinks that will take you directly to the PDB website or Uniprot website.

4.1.8 Display PDB Header

To display the PDB Header for a PDB file.

• First load a PDB file into ICM (see Load PDB)
• Double click on the word header in the ICM Workspace.

• The PDB Header information will be displayed.
• Click on the blue hyperlinked text to link to external web pages for additional information if needed.

When you search for a PDB file and load it into ICM you will see an icon (shown below) next to your protein name in the ICM Workspace. Click the icon and you will be taken directly to the PubMed primary reference relating to the structure.