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patrickbryant1 / SpeedPPI

Rapid protein-protein interaction network creation from multiple sequence alignments with Deep Learning
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using PDB/a3m as input files - SpeedPPI #11

Closed soundharramsay closed 1 year ago

soundharramsay commented 1 year ago

Can I use a PDB or a3m file as input for the SpeedPPI pipeline? If yes, how to parse multiple PDB files as input as that of a FASTA seq. ( I wish to analyze 3 PDB versus 6 PDB files)

patrickbryant1 commented 1 year ago

Hi,

You have to input the sequences of these PDB/a3m files. There is no parser for the files directly. If you have a3m files, you do not have to build the MSAs, but the sequences are present in the first (second) row of the a3m files. I suggest you read up on what these files contain since there seems to be some confusion here.

Best,

Patrick