Topics — The twenty-eight kinds of claim this anthology files against — the primary axis of both the practice registry and the reading list, and the same twenty-eight for each (ADR-026). The filing rule is the point: take a domain topic when the claim is ABOUT the domain; a claim merely discovered in one still takes its kind. The axis organizes the record, it does not bound it: content the list cannot place is evidence the list is short (ADR-059).
Biomolecular modeling — models whose data is molecules — protein and nucleic-acid structure prediction, biological sequence language models, docking and molecular property prediction — what they get right, what their benchmarks can show, and which of their methods travel to other domains.
1 of 129 THEORY documents. Back to the full index.
| # | Title | Summary | Status |
|---|---|---|---|
| THEORY-084 | AlphaFold 2 needs the sequence alignment to find a protein’s coarse fold, not to refine it, so accuracy collapses below a minimum alignment depth and barely improves above it | Jumper et al. (2021), LIT-583 — accuracy falls steeply when the median alignment depth is below about 30 sequences and gains little above about 100. Dropping both metagenomic databases costs 6.1 GDT, almost all from a few targets losing 20 or more. The authors’ hypothesis is that covariation in the alignment is needed early, to place the coarse fold, and that refinement to atomic accuracy does not depend on it. The threshold is measured. The two-stage account is not tested. | Proposed |