Supplementary_File_S1

README – AlphaFold3-Predicted VHH–EGFR Complexes This archive contains the AlphaFold3-predicted structural models of EGFR in complex with single-domain antibodies (VHHs) used in the study: "Allosteric Antibody Modulation of EGFR Activity: Bridging Experiment and In Silico Modeling" Fournier et al., 2025Description Each subdirectory corresponds to a VHH–EGFR modeling condition, named by VHH identity and the specific EGFR region used as input (a2_egfr_294_543, g9_egfr_1_294, e6_egfr_full, etc.). These were selected based on experimental epitope mapping (BLI) or used as control modeling conditions for assessing AlphaFold3 prediction quality. All models were generated using the AlphaFold3 webserver. For each VHH–EGFR input pair, five ranked models were produced. The folder includes the following files: Files per modeling condition:fold___model_0.cif – 3D structure of the top-ranked model...fold___model_4.cif – 3D structure of rank 5 modelfold__<i>summary_confidences</i>*.json – per-model confidence scores (pLDDT, ipTM, pae_cross)fold__<i>full_data</i>*.json – full model outputs from AlphaFold3NotesFor downstream allosteric modeling with SBSMMA, only one EGFR region per VHH was selected (indicated by the green highlighting in Supplementary Table S2).The EGFR regions used in modeling include:Full extracellular EGFR ("_full")Contiguous domain pairs (EGFR_I_II, EGFR_II_III, EGFR_III_IV)BLI-guided segmental constructs (EGFR_294_543, EGFR_1_294)All models were aligned to the full-length tethered EGFR conformation from Arkhipov et al., 2013. as showed in Figure 2 of the manuscript.