I have always used the online service of pBlast and now I am a bit confused since I want to use its standalone version. My aim is to blast a protein fasta sequence against PDB and save all the pdb codes of the resulted proteins. I am confused which files I do require from (ftp://ftp.ncbi.nih.gov/blast/) and what commands I need to use(My platform is Windows). I would be thankful if you can guide me on this.
I have read the available documents but wasn't able to get what I want.
Thanks for you help in advance.