ReCLIP Release Artifacts

This repository hosts release artifacts for ReCLIP:

Learning residue-level context for modeling protein-protein interactions

The code repository is available at:

https://github.com/SiweiLab/ReCLIP

Current Contents

classifier_heads/
  mutation/
    reclip_mutation_xgb_best_fold5_by_ROC_AUC_macro_ovr.pkl
    reclip_mutation_xgb_best_fold5_by_ROC_AUC_macro_ovr.json
  ptm/               Placeholder for PTM classifier heads
  peptide_mhc/       Placeholder for peptide-MHC classifier heads

figure_data/
  mutation/          Placeholder for release figure tables
  ptm/               Placeholder for release figure tables
  peptide_mhc/       Placeholder for release figure tables
  interpretation/    Placeholder for interpretation analysis tables

metadata/            Model configuration, feature schema, checksums, and notes

Mutation Classifier Head

The uploaded mutation artifact is the best-fold XGBoost classifier head selected by macro one-vs-rest AUROC on the four-class mutation effect prediction task. It expects features produced by the ReCLIP mutation pipeline with the validated setting: ESM2 layer 32, top-k 5 residues per head, context features with layer normalization, flattened target representation, and MINT partner representations.

Artifact	Description
classifier_heads/mutation/reclip_mutation_xgb_best_fold5_by_ROC_AUC_macro_ovr.pkl	XGBoost classifier head
classifier_heads/mutation/reclip_mutation_xgb_best_fold5_by_ROC_AUC_macro_ovr.json	Metadata, metrics, XGBoost parameters, and checksum

Key metadata:

• Best fold: 5
• Selection metric: ROC_AUC_macro_ovr
• Best-fold AUROC: 0.973531
• Feature dimension: 7680
• SHA256: 8744392e55c067903ffefcb5fd0862a7b1f971043f211b8f26bb8c87f89cbb16

Planned Additions

Additional PTM and peptide-MHC classifier heads, together with larger reproducibility artifacts, will be added after journal submission.

Citation

The manuscript is currently in preparation. Citation details will be updated after the preprint or final publication is available.

@misc{reclip2026,
  title = {Learning residue-level context for modeling protein-protein interactions},
  author = {ReCLIP authors},
  year = {2026},
  note = {Manuscript in preparation}
}

License

License information will be finalized before public release.