Hi, I would like to perform a virtual screening for tetramers on a protein of interest. For this purpose, I randomly generate thousands of different tetramer peptide sequences in FASTA format and I need to convert them into PDB format. With Swiss PDB Viewer, it is only possible to perform the FASTA-->PDB conversion one by one as the program does not allow to upload more than one sequence at once. I am looking for a script or Unix commands to perform multiple FASTA-->PDB conversions but I have not found a solution yet. So I am wondering if it is possible to convert FASTA files into PDB format in a script, or can I execute the "load sequence from aminoacids" and then "save current layer" functions by using for instance shell.exec () function? I appreciate your help. Thank you. Best Regards
You can use Pymol with the build_seq.py script.
EDIT: Actually, you can easily build a pipeline using Biopython to parse the FASTA files (here), then pass this to pymol and create the 3D structure in whatever secondary structure you want (coil for you I guess) using the build_seq.py script. This should be a 20 line script or so, we use it in the lab to generate peptide structures from sequence.
I'm just curious about one thing: Do you need to generate all the possible 20^4 (1,60000) possible tetra peptides and get their structures from Seq->PDB, ( with an energy minimization possibly), or, you wish to get all the tetra peptide structures that can be be found in protein structures that are available in (non-redundant,highresolution ) PDB?
Sorry for the late reply, I have just seen your question. Firstly I created random short peptide sequences by R programming. The random peptide sequences were written in a txt. file. By using the "build_seq" script, I was able to create short peptide sequences written in the txt. file. I created the PDB structures for each sequence afterwards. So you can write a short python script to read the sequences from txt.file and to run the "build_seq" script automatically for each peptide sequence.
I hope this answer would be helpful.