Tunnel Architecture as a Structural Determinant of Peptide–Enzyme Binding Mode — Comprehensive Data Package

Comprehensive data package for: "Tunnel Architecture as a Structural Determinant of Peptide–Enzyme Binding Mode: A Two-Layer Framework Integrating Pocket Enclosure and Channel Geometry across Xanthine Oxidase, Prolyl Endopeptidase, Angiotensin-Converting Enzyme, and Dipeptidyl Peptidase IV" Prepared for submission to the Journal of Molecular Graphics and Modelling. VERSION 2 UPDATE: Repository substantially expanded from ~600 to 1,088 files. Added: (1) mutagenesis docking results (102 AutoDock Vina files for 4 enzymes × WT + 3 alanine mutants × 5 peptides), (2) XO dual-site FAD/MoPt docking for 23 peptides + 3 reference compounds across apo/holo conditions (377 files), (3) Dataset S1 (15-sheet Excel workbook), (4) file manifest linking repository directories to manuscript tables/figures. Topology note clarified: GROMACS-format .top/.itp files (not NAMD .psf). CONTENTS OF zenodo_complete_JPCB.tar.gz:- Dataset_S1_FINAL.xlsx (15 sheets: master data, CAVER tunnels, fpocket, literature survey, mutagenesis docking, peptide diameters, conformer robustness, MD tunnel dynamics, RMSD)- README.md (full documentation)- file_manifest.csv (directory-to-table/figure mapping)- caver_configs/ (CAVER 3.0 configuration files)- caver_results/ (MD tunnel dynamics output, 101 frames × 4 enzymes)- md_parameters/ (GROMACS em/nvt/npt/md .mdp files)- topology/ (GROMACS .top and .itp files for 4 enzyme–peptide complexes)- fpocket_output/ (fpocket 4.1 output for 4 representative structures)- docking_output/ (AutoDock Vina MD starting poses)- xo_docking/ (XO dual-site docking, 377 files)- mutagenesis_docking/ (alanine scanning docking, 102 files)- alanine_scan/ (gmx_MMPBSA XO F914A analysis)- rmsd_*.xvg (backbone RMSD time courses)