IEEE/ICACT20250017 Slide.07        [Big Slide]       [YouTube] Oral Presentation
Now, we formally define the protein scaffold filling problem: Given a target protein sequence T (which is unknown) and a protein scaffold S with m contigs (fragments) labeled S1 through Sm, our objective is to fill the missing amino acids between these contigs to obtain a completed sequence S' that maximizes correctly matched amino acids with the target sequence. As shown in the diagram, we have multiple contigs (S1, S2, S3, S4) with gaps between them. Our challenge is to predict the sequences in these gaps to complete the scaffold.

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