Disclosure: I run rewire.it , where I published the article linked below. A FASTA sequence does not fully specify a protein-structure prediction job. A single chain, a protein assembly and a protein–ligand complex require different inputs and validation. Database versions, alignments, templates and the sampling protocol also change what was actually tested. Confidence scores need the same distinction. Local confidence, relative domain placement and interface confidence concern different aspects of the predicted geometry. None is a measurement of catalytic activity or binding in a particular assay. Drawing more diffusion samples can explore candidate structures, but those samples are not automatically a thermodynamic ensemble. I wrote a guide to those choices, including what to record before comparing models or interpreting their scores: https://rewire.it/blog/a-fasta-file-is-not-a-specification/ The useful evaluation question is which biological claim the output supports. What evidence would you require before carrying a model-selected structure into a downstream functional claim? submitted by /u/Fair-Rain3366
Originally posted by u/Fair-Rain3366 on r/ArtificialInteligence