Protein-Looking Is Not Fold-Aware
Masked sequence models are good at producing plausible amino acids. Plausible is not the same as compatible with the residues that must meet in three-dimensional space.
foldcontact builds paired residue constraints, masks one side of every contact, and asks two infillers to rebuild it. One samples from the amino-acid alphabet. The other must satisfy the contact class.
The Contact Map Gets A Vote
The guided decoder treats hydrophobic, charged, and polar compatibility as a hard selection signal. Every prediction remains inspectable; there is no checkpoint hiding the decision.
This is a small reproduction of a structure-aware design idea, not a structure predictor. It exists to isolate the value of geometric constraints before scaling the architecture.
The Number
Random infilling satisfies 34.5% of 1,440 held-out contacts. Contact-guided infilling satisfies 100%, a 65.5-point gain.
The controlled benchmark is educational and not a wet-lab claim. One deterministic test passes across the three-version GitHub Actions matrix.
Research Basis
Inspired by the 2025 AtomWorks and RosettaFold-3 release. The portfolio number above comes from this repository's own controlled benchmark, not from the paper.