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

April 26, 2017blast database in-house incorporated pdb Prime structures

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

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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: • Create a single fasta file containing all your in-house sequences. • 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. • 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. • Import the results, query_blast.out, into Prime.