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I can find any number of base pair nucleotide sequences for any number of genes in the fasta format. (Check out the COSMIC Tumor Database, for example). I'm having trouble finding base pair nucleotide sequences in the pdb (Protein Data Bank) format. As a result, I am not able to generate three dimensional images of the genes of my choice. Is there any hope? Does Mathematica convert fasta format files to pdb format files? Is there a link somewhere in Mathematica giving me access to a treasure trove of gene images (pdb files) in three dimensions?

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    $\begingroup$ PDB files contain 3D structure information, do FASTA files? If not, then you need to generate the structure information from the FASTA. There's this post, but the two answers there either require you to have the PDB already, or to have a pure DNA sequence. Mathematica can't generate 3D structure information at the moment. $\endgroup$
    – Jason B.
    Commented Nov 29, 2016 at 20:48
  • $\begingroup$ It looks like the rdKit handles FASTA files, and I know that it can generate 3D coordinates. You might have to use a bit of python to get it to work. $\endgroup$
    – Jason B.
    Commented Nov 29, 2016 at 21:05

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