Can in-house PDB structures be incorporated into the BLAST database for use with Prime?

In-house PDB structures cannot be incorporated directly into the BLAST database for use with Prime. However, you can create a BLAST database of your own PDB structures and use it to find homologs, then import the hits into the Prime Comparative Modeling workflow, as follows:

1. Create a single fasta file containing all your in-house sequences.
2. Create a blast db using the following command:
   
   $SCHRODINGER/thirdparty/bin/Linux-x86/blast/bin/formatdb -p T -o T -n "inhouseseq" -i inhouseseq.fasta
   
   The name of the database is set with the -n option.
3. Search the new database using the following command:
   
   $SCHRODINGER/thirdparty/bin/Linux-x86/blast/bin/blastall -p blastp -d inhouseseq -m 9 -i query.fasta -o query_blast.out
   
   If the files created in step 2 are not in the current directory when you run the search, you must use the full path name with the -d option.
4. Import the results, query_blast.out, into Prime.

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