Supplemental Information for Structure-Based Discovery of Heparanase Inhibitors from Tetrasaccharide Aminoglycosides

Classical_MD_Input_Files.zip: Contains topology and starting coordinates for each docked ligand simulation tested.  Also contains input files for use with Amber20, following the order "init", "cold_equil", "heating", "hot_equil", and finally "production".  Each stage with numerical filenames follows iterative relaxation of restraints.

Classical_MD_Replicate_Analyses.zip: Contains example input file for cpptraj analysis (all simulations followed the same pattern, only the incoming topology and trajectory files differ) as well as replicate results for RMSD, RMSF, Correlated Motion, and Hydrogen Bonding, all separated by ligand.  Also includes example final frame from a representative trajectory for each ligand.

Docked_Ligand_Poses.zip:  Contains the PDB structure of each ligand docked to heparanase produced by Yasara.

Free_Ligand_Structures.zip:  Contains the PDB structure of each ligand before docking.

Ligand_Forcefield_Parameters.zip:  Contains the .mol2 and .frcmod files generated by AutoParams for each ligand simulated.  These files are necessary to regenerate the MD topology and starting coordinates provided in Classical_MD_Input_Files.zip

Heparanase_Ligands_SMILES.csv: Comma-Separated Values file containing the SMILES strings for each ligand tested.

Yasara_MD_Inputs_and_Analysis.zip: Contains Yasara inputs, md scripts, and analysis scripts for all tested ligands.