DOI: 10.5281/zenodo.4307997
title: Data for the article: "Molecular Modelling Reveals Eight Novel Druggable Binding Sites in SARS-CoV-2's Spike Protein" by Ilke Ugur and Antoine Marion

description: This upload contains data related to the article<br> published as a preprint on ChemRxiv with DOI<br> https://doi.org/10.26434/chemrxiv.13292768 "Molecular Modelling Reveals Eight Novel Druggable Binding Sites in SARS-CoV-2's Spike Protein"<br> by Ilke Ugur and Antoine Marion (2020)<br> Department of Chemistry, Middle East Technical University, Ankara, Turkey. For further information, please contact:<br> ilkeugur@metu.edu.tr ; amarion@metu.edu.tr The manuscript is currently under peer-review. Content: Library of molecules derived from DrugBank v 5.1.5:<br> - DrugBank_2020_5.1.5/ # All necessary files for the docking and refinement of the library of molecules.<br> -- DB_5.1.5_pH7.4_pdbqt/ ## PDBQT readily usable for docking with AutoDock Vina.<br> -- DB_5.1.5_pH7.4_mol2amber/ ## mol2 files containing assigned GAFF atom types and Gasteiger atomic charges.<br> -- DB_5.1.5_pH7.4_frcmod/ ## frcmod files containing missing molecular mechanics parameters<br> -- dbID_name.dat ## DrugBank ID to generic name dictionary Note: The files were prepared automatically via a series of operations handling openbabel and antechamber.<br> The protonation state of ionizable groups as well as Gasteiger atomic charges were assigned by openbabel for a pH of 7.4<br> mol2 and frcmod files can be used readily via the tleap module of AmberTools to produce topology files. <br> Receptor structures:<br> - receptors/ # PDB files for the four structures of the spike protein considered in this work<br> -- CS00ns.pdb ## Closed state after the remodelling of missing loops (PDB ID 6vxx)<br> -- OS00ns.pdb ## Open state after the remodelling of missing loops (PDB ID 6vyb)<br> -- CS25ns.pdb ## Closed state after 25 ns of molecular dynamics in explicit water<br> -- OS25ns.pdb ## Open state after 25 ns of molecular dynamics in explicit water Note: All structures are aligned to CS00ns.pdb and can be converted to pdbqt for docking with AutoDock Vina <br> Docking grid centers:<br> - dockingCenters/ # XYZ files containing the coordinates of each docking grid center considered in this work Note: The coordinates are given in the same frame as that of the four structures of the receptor. <br> Binding sites:<br> - bindingSites/ # XYZ files with the coordinates of the representative atomic centres<br> # of each binding site identified in this work (A-H). Note: These files can be used to get a clearer picture of the binding sites within the structures<br> of the spike protein shared in the receptors directory. <br> Final modelling results:<br> - allData.txt # data for all molecules in the set (approved and investigational)<br> - appData.txt # data for approved molecules only<br> - data.xlsx # data for all molecules in the set (approved and investigational)<br> # as a formatted excel spreadsheet Note: The columns are delimited with semi-colons ";".<br> The files contain the results for the best pose of all approved molecules for which<br> molecular mechanics-based geometry optimization succeeded, regardless of their score.<br> For other molecules, the result of their best pose is reported only for those complexes<br> having MM interaction energy lower or equal to -22.00 kcal/mol. <br> Visualization:<br> - bs.pse # pymol session representing the binding sites within the<br> # closed state structure of the spike protein (CS00ns)<br> - pt.pse # pymol session representing the docking grid centres within<br> # closed statestructure of the spike protein (CS00ns) Note: the PSE files should be compatible with version 7.0 of pymol and later