Water-Guided Docking Improves Prediction of Protein–Glycan Complexes - Supporting Information

Lannot et al. (2025): Water-Guided Docking Improves Prediction of Protein–Glycan Complexes - Supporting Information The available dataset is organized into 30 systems, each identified under the nomenclature HoloID_ApoID. Within each system folder, the basic input files required to perform the docking runs are provided, with intuitive filenames for ease of use: reference_ligand.pdbqt: the ligand prepared in AutoDock-compatible .pdbqt format, on the reference pose from the holo complex randomized_ligand.pdbqt: the ligand prepared in AutoDock-compatible .pdbqt format, on a randomized pose holo_receptor.pdbqt: the holo conformation of the receptor, prepared and saved in .pdbqt format. apo_receptor.pdbqt: the apo conformation of the receptor, structurally aligned to its holo counterpart, prepared and saved in .pdbqt format. af3_receptor.pdbqt: the AlphaFold3-predicted conformation of the receptor, structurally aligned to the holo receptor and prepared in .pdbqt format. config_file.conf: the configuration file containing the input parameters required to perform docking runs with ADV and the derivative versions of the software used in this study. In addition, for selected representative systems, a sites.conf file is included. This file defines the WII sites employed in the WIIGA protocol, enabling reproducibility of the guided docking experiments. Representative systems were chosen based on ligand size and include the following: 4LBN_3ZSM – tetrasaccharide 3ACI_3ACF – pentasaccharide 5XUL_5XTJ – hexasaccharide 1DMB_1JW4 – heptasaccharide 3INA_3IMN – octasaccharide 7NOX_7O8C – nonasaccharide