Molecular dynamic features of AlphaFold predicted structures of protein-protein interactions

This data repository contains the features which are used to analyze protein-protein interaction (PPI) interfaces involving transmembrane proteins, expecially Solute carrier (SLC). Protein-protein interactions were obtained from the human solute carrier (SLC) interactome (Frommelt et al. 2025, https://doi.org/10.1038/s44320-025-00109-1). Complex structures were predicted using AlphaFold v3, filtered based on model confidence, and refined by molecular dynamics simulations. Residue-level physicochemical properties, interface contacts, and structural features were subsequently extracted from the simulation trajectories for downstream analyses. The archive contains the following files: mlDIA_Contacts_T4.zip – Interface contact data derived from the MD simulations for all analyzed protein complexes. mlDIA_AA_residue_properties.zip – Per-residue physicochemical and structural properties calculated for all residues in the predicted protein complexes. reference_dataset.zip – An external reference dataset (Burke et al. 2023, https://doi.org/10.1038/s41594-022-00910-8) used to assess the generalizability of the analyses beyond the human solute carrier (SLC) interactome. This archive contains two directories: one with the 2026_.csv summary file and one containing the interface files corresponding to each experiment. aggregated_features_RAW_untransformed.csv: Contains the aggregated features per interface which are used for analyzing the PPIs. It also contains the Alphafold values per PPI which are not aggregated. Each archive includes an accompanying .ods file that provides a detailed description of the contained files, variables, and data formats. The datasets enable reproduction of the interface-level analyses and facilitate further investigation of physicochemical properties associated with transmembrane protein-protein interaction interfaces.