GeoEF-Aff: Source Code, Trained Model, Data Splits, and Reproducibility Files

This record contains the reproducibility package for the manuscript “GeoEF-Aff: Mutation-Local Perturbation Modeling for Protein-Protein Binding Free-Energy Prediction”. The archive includes the source code, trained model checkpoint, exact sample-level three-fold cross-validation splits, validation prediction outputs, external test files, case-study input files, configuration files, and scripts required to reproduce the main computational analyses reported in the manuscript. The included model checkpoint is provided in checkpoints/best_model.pth, with its SHA256 checksum reported in checkpoints/best_model.pth.sha256. The data_splits directory contains the exact train/validation split files and full split manifest used for the three-fold cross-validation experiments. The predictions directory contains out-of-fold validation predictions and cross-validation summary files. The external_tests and casestudy directories contain the input files used for the RBD and antibody-optimization case-study evaluations included in the final submitted package. This Zenodo archive is intended to serve as the version-of-record reproducibility package associated with the manuscript. The development repository is available at https://github.com/huzerong/GeoEF-Aff.