Simulation results for Sars-CoV2 3C-like main protease: TRAPP analysis of the binding site flexibility and results of the docking study

Collection of data and scripts related to the paper:

Jonas Gossen et al. "A blueprint for high affinity SARS-CoV-2 Mpro inhibitors from activity-based compound library screening guided by analysis of protein dynamics" 

https://www.biorxiv.org/content/10.1101/2020.12.14.422634v2   doi: https://doi.org/10.1101/2020.12.14.422634

ACS Pharmacology and Translational Science  2021 DOI: 10.1021/acsptsci.0c00215

1. TRAPP simulation results for Sars-CoV2 3C-like main protease:

include simulation of the binding pocket druggability, physical-chemical properties,  and the binding site composition

Protease_clean.ipynb  - Jupyter Notebook containing  analysis of the generated data

allTables.zip  - results of TRAPP simulations of the binding site flexibility using LRIP and tConcoord methods

Every10-ligand_6LU7_R3.5.zip - results of TRAPP pocket analysis on the MD frames

PDB-Giulia.zip - TRAPP pocket analysis of 40 PDB complexes of main protease

TRAPP_properties_PDB.xlsx - binding pocket properties for 40 PDB complexes of main protease summarized in a table

DrugPDB_3structures.xlsx - binding pocket properties for 3 PDB structures 

2. Docking & Screening Results

TRAPP_secondSelection_VS.csv - docking/screening of selected structures from TRAPP analysis

Fred_VS.csv - docking of PDB structures using Fred

Glide_VS.csv - docking of PDB structures using Glide

TableS1.xlsx -  Available structures of SARS-CoV-2 Mpro selected for binding site analyses. 

TableS2A.xlsx - SiteScore analysis of all the deposited X-ray crystal structures for the Mpro.

TableS2B.xlsx -  SiteScore analysis of the MSM ensemble (4-macrostates).