saw42@bath.ac.uk 05-March-2020

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.

The Elnemo elastic network structure software is available online from http://www.sciences.univ-nantes.fr/elnemo/

The FIRST rigidity analysis software, including the FRODA geometric simulation engine, should be available from flexweb.asu.edu. If there are difficulties obtaining the software from this source, please contact Dr. Stephen Wells (saw42@bath.ac.uk) who can provide a copy of FIRST for academic users.

The SBFIRST code for identication of covalent and noncovalent interactions in a protein structure is included in this collection of data.

The Elnemo website includes comprehensive citations for the Elnemo elastic network method and software. The primary citation for the SBFIRST identification of interactions is DOI:10.1088/1478-3975/ab2b5c (MacManus, Wells, Walker 2019). The primary citation for the use of Elnemo/FIRST/FRODA in combination is DOI:10.1088/1478-3975/9/1/016008 (Jimenez-Roldan, Freedman, Roemer, Wells 2012) and a detailed discussion of the method can be found as DOI:10.1007/978-1-62703-658-0_10 (Wells 2014). The primary citation for the FRODA geometric simulation engine is DOI:10.1088/1478-3975/2/4/S07 (Wells, Menor, Hespenheide, Thorpe 2005). The primary citation for the FIRST rigidity analysis software is DOI:10.1002/prot.1081 (Jacobs, Rader, Kuhn, Thorpe 2001).