Dear All, Sorry to be disturbing you with my new inquiry. I always got great and trustworthy results using FUGUE (Protein homology recognition using environment-specific amino acid substitution tables: https://mizuguchilab.org/fugue/prfsearch.html) I use an amino acid sequence of a viral protein of an unknown structure and function and with FUGUE it searches a structural database and gives very good results. When I use the protein BLAST for the same amino acid sequence, I may miss or get no results, especially when the identity is about 25% between the viral protein and the host protein it mimics . I tested that with a viral protein with known structure, and protein BLAST was not helpful. The only issue is that using FUGUE can be time consuming especially if I am searching for the possible function/structure of 100 viral proteins of one viral strain, not to mention that the same virus has several strains.What would be an efficient way to look for host protein mimics? I would greatly appreciate any suggestion.Thank you in advance.Best regards,Samer
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