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  1. IGB
  2. IGBF-4141

Explore Alpha Fold for purpose of applying to de novo proteins

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        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
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          Description

          GOAL: Since we have de novo proteins structures, we can look into using alpha fold to get a 3D model for any given putative protein.

          Explore Alpha Fold. Figure out what we need to do to make it happen.
          Explore time!

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              bbendick Brandon Bendickson added a comment -

              Alpha fold is pretty straight forward and easy to use. You can paste the peptide sequence directly into the website, and it runs blastp to find matching protein sequences. It provides a list of matches from highest % similarity to lowest and even displays the alignments. You can click on any match and view the proteins structure and download the associated files (PDB, mmCIF, predicted aligned error). Also provides organism, geneid, protein name (if applicable) and uniprot ID/link. A cool feature is that is also provides similar proteins and performs structure similarity clustering. Only downside is it takes around 10 minutes depending on size of sequence. It is very cool to see our 3D denovo proteins!

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              bbendick Brandon Bendickson added a comment - Alpha fold is pretty straight forward and easy to use. You can paste the peptide sequence directly into the website, and it runs blastp to find matching protein sequences. It provides a list of matches from highest % similarity to lowest and even displays the alignments. You can click on any match and view the proteins structure and download the associated files (PDB, mmCIF, predicted aligned error). Also provides organism, geneid, protein name (if applicable) and uniprot ID/link. A cool feature is that is also provides similar proteins and performs structure similarity clustering. Only downside is it takes around 10 minutes depending on size of sequence. It is very cool to see our 3D denovo proteins!

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                • Assignee:
                  bbendick Brandon Bendickson
                  Reporter:
                  robofjoy Robert Reid
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                    Updated:
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