Auditable Algebraic Counting Field for Cryptic-Pocket Detection from Apo Structures

Shan Yu, Xuening Wu

Cryptic ligand-binding pockets are not apparent in experimentally determined apo structures, making them difficult to identify from unbound receptor geometry. A complementary challenge is to make the structural measurements and learned evidence behind each prediction directly inspectable. We introduce a supervised algebraic counting field (ACF) for predicting cryptic-pocket residues from apo structures. ACF compiles explicit geometric, physicochemical, and topological features into compact, integer-weighted lookup tables. Each prediction score can be reconstructed from feature values, training counts, table weights, and spatial aggregation, without sequence search, structural-template transfer, or a protein language model at inference. We evaluate ACF on CryptoBench and two locked external collections, separating ranking performance from the effects of residue-calling budgets. On an external set of 57 post-CryptoBench apo-holo units, ACF exceeded P2Rank by +0.044 in mean paired ROC-AUC (multiplicity-adjusted 95% CI [+0.010, +0.079]). The advantage was dataset-dependent: official-fold ROC-AUC and matched-budget F1 differences against P2Rank remained unresolved, and a second…