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).