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The PDB search tab provides easy access to the PDB database. You can use keyword searching or type in the PDB code you are interested in. An asterisk (*) wildcard can be used to list all the pdb files currently available in the protein databank. Different fields can be searched by using the drop down arrow as shown below. More advanced PDB search tools and how to use the PDB search result table are described in the section entititled Searching the PDB.
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
Or
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:
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.
4.1.1.3 Query PDB by Ligand Code |
To query the PDB by ligand code:
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
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:
OPTION 2:
If your PDB sequence is not loaded into ICM:
NOTE: If you merely want to see the PDB codes which are similar to your sequence then un-check the Load Sequences box. |
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.
NOTE: In the table there are blue hyperlinks directing you to the PDB and Uniprot websites. |
4.1.4 Loading Your PDB File |
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.
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.
4.1.9 Direct link to PubMed |
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.
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