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

This upload contains data related to the article
published as a preprint on ChemRxiv with DOI
https://doi.org/10.26434/chemrxiv.13292768

"Molecular Modelling Reveals Eight Novel Druggable Binding Sites in SARS-CoV-2's Spike Protein"
by Ilke Ugur and Antoine Marion (2020)
Department of Chemistry, Middle East Technical University, Ankara, Turkey.

For further information, please contact:
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:
- DrugBank_2020_5.1.5/        # All necessary files for the docking and refinement of the library of molecules.
-- DB_5.1.5_pH7.4_pdbqt/      ## PDBQT readily usable for docking with AutoDock Vina.
-- DB_5.1.5_pH7.4_mol2amber/  ## mol2 files containing assigned GAFF atom types and Gasteiger atomic charges.
-- DB_5.1.5_pH7.4_frcmod/     ## frcmod files containing missing molecular mechanics parameters
-- dbID_name.dat              ## DrugBank ID to generic name dictionary

Note: The files were prepared automatically via a series of operations handling openbabel and antechamber.
      The protonation state of ionizable groups as well as Gasteiger atomic charges were assigned by openbabel for a pH of 7.4
      mol2 and frcmod files can be used readily via the tleap module of AmberTools to produce topology files.

Receptor structures:
- receptors/                  # PDB files for the four structures of the spike protein considered in this work
-- CS00ns.pdb                 ## Closed state after the remodelling of missing loops (PDB ID 6vxx)
-- OS00ns.pdb                 ## Open   state after the remodelling of missing loops (PDB ID 6vyb)
-- CS25ns.pdb                 ## Closed state after 25 ns of molecular dynamics in explicit water
-- 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

Docking grid centers:
- 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.

Binding sites:
- bindingSites/               # XYZ files with the coordinates of the representative atomic centres
                              # 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
      of the spike protein shared in the receptors directory.

Final modelling results:
- allData.txt                 # data for all molecules in the set (approved and investigational)
- appData.txt                 # data for approved molecules only
- data.xlsx                   # data for all molecules in the set (approved and investigational)
                              # as a formatted excel spreadsheet

Note: The columns are delimited with semi-colons ";".
      The files contain the results for the best pose of all approved molecules for which
      molecular mechanics-based geometry optimization succeeded, regardless of their score.
      For other molecules, the result of their best pose is reported only for those complexes
      having MM interaction energy lower or equal to -22.00 kcal/mol.

Visualization:
- bs.pse                      # pymol session representing the binding sites within the
                              # closed state structure of the spike protein (CS00ns)
- pt.pse                      # pymol session representing the docking grid centres within
                              # closed statestructure of the spike protein (CS00ns)

Note: the PSE files should be compatible with version 7.0 of pymol and later