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

Authors: Daria Kokh; Jonas Gossen; Simone Albani; Anton Hanke; Benjamin P. Joseph;

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

Abstract

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 Results TRAPP_secondSelection_VS.csv - docking of selected structures from TRAPP analysis Fred_VS.csv - docking of PDB structures using Fred Glide_VS.csv - docking of PDB structures using Glide

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citations
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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
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influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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