To BLAST the NCBI sequence database (including PDB sequences):

• Go to the Search tab
• Choose the drop down option for BLAST and follow the instructions here.

To BLAST search a local BLAST formatted file:

ICM provides a fast tool to search any Blast-formatted database with a query sequence and generate an alignment on the fly. For example you can use this option to find template structures for homology modeling.

1. Select Bioinfo/Search and Align (or right click on a sequence)
2. Enter the sequence name you wish to search against the database with.
3. Locate the blast-formatted database to search. You can download Blast formatted databases from here ftp://ftp.ncbi.nih.gov/blast/db/ eg. pdbaa - PDB sequence database.
4. Specify the speed parameter (0 is the slowest, but the most detailed, 100 is the fastest search for nearly identical sequences).
5. Enter the number of hits you would like to view
6. Enter an identity threshold filter to narrow down the number of hits.
7. The top hits will be displayed in a table.