Dataset for "Rigidity, normal modes and flexible motion of a SARS-CoV-2 (COVID19) protease structure"

This file contains simulations and analysis carried out on two protein structures from the SARS-CoV-2 (COVID19) virus. These structures are PDB entries 6Y2E and 6LU7. Both structures represent the same homodimeric protease. 6Y2E represents the free protease while 6LU7 includes a bound inhibitor, N3.

The folder for each structure includes README files at each level describing how the structure has been processed and what results have been produced. This study includes rigidity analysis of the crystal structures, elastic network modelling to identify normal modes of the structures, and all-atom geometric simulations of flexible motion along normal mode directions. This study makes use of the PDB, the MolProbity structure processing webserver, FIRST rigidity analysis software, the FRODA geometric simulation engine, Elnemo elastic network modelling software, and PyMOL visualisation software. The SBFIRST code for identication of covalent and noncovalent interactions in a protein structure is included in this collection of data.