Complete Donor-Set Guidance for Frozen Diffusion Docking Models
Abstract
Metalloprotein docking requires a ligand pose to satisfy both global pocket fit and the identity and geometry of metal-coordinating atoms. General-purpose diffusion docking models do not explicitly condition generation on externally specified complete ligand donor sets, and their predicted poses can exhibit incorrect metal-donor relationships. Metal-aware models address coordination during training and generation; here we ask whether external donor information can correct already-trained general-purpose models without retraining. We propose Complete-Identity Contract Guidance (CICG), which applies a supplied complete donor set through translation, rotation, and torsion updates, and Historical Contract Transfer (HCT), which supplies donor identities from earlier complexes at compatible receptor sites. We compare HCT with trajectory-local controls retaining the historical donor count with or without elemental composition. On 86 assessable HCT-covered queries, HCT-guided CICG increases frozen-confidence-selected joint success from 21.5% to 36.6% on SurfDock and from 25.0% to 34.9% on DiffDock-L. The joint criterion requires correct global ligand placement, complete native donor recovery, coordination geometry, preserved stereochemistry, and absence of fatal receptor clashes. Composition-matched guidance reaches 33.14% and 34.30%, leaving the additional benefit of fixed historical membership unresolved. Our results therefore support donor-set guidance as a conditional correction for frozen docking models, while identifying donor-source reliability and physical-quality preservation as the main barriers to broader use.
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BibTeX
@misc{kim2026complete,
title = {{Complete Donor-Set Guidance for Frozen Diffusion Docking Models}},
author = {Hyunwoo Kim and Insoo Park and Ziseok Lee and Wooyeol Lee and Yoorim Gang and Kyungsu Kim},
howpublished = {arXiv},
year = {2026},
month = nov,
doi = {10.48550/arxiv.2611.03731},
eprint = {2611.03731},
archivePrefix = {arXiv},
url = {https://arxiv.org/abs/2611.03731},
note = {CC BY 4.0},
}
RIS
TY - UNPB
TI - Complete Donor-Set Guidance for Frozen Diffusion Docking Models
AU - Hyunwoo Kim
AU - Insoo Park
AU - Ziseok Lee
AU - Wooyeol Lee
AU - Yoorim Gang
AU - Kyungsu Kim
PY - 2026
DA - 2026/11/01
PB - arXiv
DO - 10.48550/arxiv.2611.03731
UR - https://arxiv.org/abs/2611.03731
AB - Metalloprotein docking requires a ligand pose to satisfy both global pocket fit and the identity and geometry of metal-coordinating atoms. General-purpose diffusion docking models do not explicitly condition generation on externally specified complete ligand donor sets, and their predicted poses can exhibit incorrect metal-donor relationships. Metal-aware models address coordination during training and generation; here we ask whether external donor information can correct already-trained general-purpose models without retraining. We propose Complete-Identity Contract Guidance (CICG), which applies a supplied complete donor set through translation, rotation, and torsion updates, and Historical Contract Transfer (HCT), which supplies donor identities from earlier complexes at compatible receptor sites. We compare HCT with trajectory-local controls retaining the historical donor count with or without elemental composition. On 86 assessable HCT-covered queries, HCT-guided CICG increases frozen-confidence-selected joint success from 21.5% to 36.6% on SurfDock and from 25.0% to 34.9% on DiffDock-L. The joint criterion requires correct global ligand placement, complete native donor recovery, coordination geometry, preserved stereochemistry, and absence of fatal receptor clashes. Composition-matched guidance reaches 33.14% and 34.30%, leaving the additional benefit of fixed historical membership unresolved. Our results therefore support donor-set guidance as a conditional correction for frozen docking models, while identifying donor-source reliability and physical-quality preservation as the main barriers to broader use.
ER -