I have some sequences of Spike protein of some Covid 19 samples that have been sequenced in my laboratory using NGS. For analyses of those, I need to convert those sequences into PDB format. I am using Windows 10 Pro. Can any expert suggest to me how can I do that?
I think It is not possible to convert amino acid sequence directly into PDB.
Hi,
PDB file is a 3D structure format with x, y, z co-ordinates and is obtained by x-ray crystallography , cryo-EM, NMR and so converting aminoacids to PDB in your case can be done by protein modelling. And if I am correct, there are structures available for Spike Protein of SARS-COV-2 in RCSB-PDB website. You can use them. And also you can compare the sequence of the structure that you obtain from PDB website with your own NGS sequences. If there are variations, you can also model those using the RCSB-PDB structure as template and the variant sequence as query in I-tasser. I hope this helps for you.
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