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.

README — AlphaFold3预测的VHH–EGFR复合物数据集

本存档包含本研究《变构抗体调控EGFR活性：架接实验与硅基建模》（"Allosteric Antibody Modulation of EGFR Activity: Bridging Experiment and In Silico Modeling"）中所使用的、与单域抗体（Variable domain of heavy chain antibody, VHH）结合的表皮生长因子受体（Epidermal Growth Factor Receptor, EGFR）的AlphaFold3预测结构模型，作者为Fournier等人，发表于2025年。

数据集说明
每个子目录对应一组VHH–EGFR建模条件，命名规则为VHH标识与用作建模输入的特定EGFR区域（如a2_egfr_294_543、g9_egfr_1_294、e6_egfr_full等）。此类建模条件或基于实验表位图谱（生物层干涉术，Bio-layer Interferometry, BLI）筛选获得，或作为对照条件用于评估AlphaFold3的预测性能。所有模型均通过AlphaFold3网络服务器生成。针对每一组VHH–EGFR输入配对，共生成5个经排序的结构模型。

本文件夹包含以下类型的文件：
单建模条件下的文件包括：
fold___model_0.cif：排名第一的模型的三维结构文件
fold___model_4.cif：排名第5的模型的三维结构文件
fold__<i>summary_confidences</i>*.json：单模型置信度评分文件（包含pLDDT、ipTM、pae_cross三项指标）
fold__<i>full_data</i>*.json：AlphaFold3输出的完整模型结果文件

备注
若需使用SBSMMA开展下游变构建模，仅需为每个VHH选择一个EGFR区域（补充表S2中的绿色高亮条目已标注对应选择）。

本次建模使用的EGFR区域包括：
1. 完整胞外段EGFR（标注为"_full"）
2. 连续结构域对（EGFR_I_II、EGFR_II_III、EGFR_III_IV）
3. 基于BLI筛选的分段构建体（EGFR_294_543、EGFR_1_294）

所有模型均已与Arkhipov等人2013年发表的全长锚定型EGFR构象完成对齐，如论文图2所示。