PTM Accessibility
Quantifying how splicing rewires PTM accessibility — with confidence masking and a relative-change threshold so the calls survive a rigorous review.
For every known phosphorylation, ubiquitination, or acetylation site on the canonical isoform we project the residue onto the novel isoform via a splice-aware alignment (the same k-mer-anchored algorithm used by the MSA panel) and recompute its solvent-accessible surface area (SASA) with FreeSASA on the AF3 models.
Five-way classification
A site is reclassified only when both the absolute Δ (> 10 Ų) and the relative Δ (> 25% of the canonical SASA) clear their thresholds, and when the minimum pLDDT across the two structures is ≥ 70. Otherwise the call stays at "intact" or "undetermined" — we'd rather be honest about uncertainty than inflate the count of regulatory rewirings.
Site retained with no meaningful accessibility change.
Site moved into a more solvent-accessible state — both the absolute and relative thresholds must clear.
Site moved into a more solvent-shielded state. A conformational reshuffle or domain insertion.
Splice-aware alignment maps the canonical position to a gap in the novel — the residue is not in the protein at all.
SASA could not be computed for one or both structures, OR the residue lies in a low-confidence region of the AF prediction. Side-chain placement is unreliable here — we deliberately refuse to call exposed/buried.
Why a relative threshold matters
Baseline SASA varies an order of magnitude across residues — a fully-buried residue can have ~5 Ų, a fully-exposed surface residue ~150 Ų. An absolute ±10 Ų rule labels the same physical shift as "huge" in one case and "noise" in the other. Requiring a simultaneous ±25% relative change calibrates the call to the residue's own baseline. The combined rule was chosen because:
- Either threshold alone produced false positives at the extremes (relative-only over-called buried residues; absolute-only over-called exposed residues).
- The legacy "unchanged" bucket conflated true non-change with cases where SASA simply couldn't be computed. Those rows are now undetermined, distinguishable in both the UI and the API.
Structural context (TED)
We tag each site with its position relative to the TED structural domain boundaries. This is contextual information — it does not change the accessibility classification.
Intra-domain
The site sits within a stable, folded domain in the novel isoform.
Disrupted
The site was inside a canonical domain that splicing fractured — no longer in a domain in the novel.
Inter-domain
The site is in a flexible linker / loop region in both isoforms, OR no TED domains were annotated.