Reproducibility archive for "Are scaffold placement and warhead placement the same achievement? Ligand RMSD and covalent geometry are independent axes in co-folding predictions"
Oct 2026· Zenodo (CERN European Organization for Nuclear Research)
Computational Drug Discovery Methods
Abstract
Data and code for a cutoff-controlled benchmark of 26 cysteine-targeted covalent protein–ligand complexes, all X-ray structures at 1.1–1.82 Å released after the Chai-1 training cutoff of 30 September 2021. Three predictors are scored on identical inputs: co-folding (Chai-1 v0.6.1), blind docking (smina, Vina scoring) and a warhead-anchored covalent-docking surrogate. Each prediction is scored on two independent axes — symmetry-corrected heavy-atom ligand pose RMSD, and the distance from the electrophilic warhead atom to the target cysteine Sγ. The archive contains the benchmark set definition, crystallographic reference data, all docked and covalent-surrogate poses, the consolidated per-complex results, and the complete scoring and figure-generation code. Co-folding predicted structures are not included; all inputs needed to regenerate them are provided. See README.md for full contents.
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