  Recent events leading to the worldwide pandemic of COVID-19 have demonstrated
the effective use of genomic sequencing technologies to establish the genetic
sequence of this virus. In contrast, the COVID-19 pandemic has demonstrated the
absence of computational approaches to understand the molecular basis of this
infection rapidly. Here we present an integrated approach to the study of the
nsp1 protein in SARS-CoV-1, which plays an essential role in maintaining the
expression of viral proteins and further disabling the host protein expression,
also known as the host shutoff mechanism. We present three independent methods
of evaluating two potential binding sites speculated to participate in host
shutoff by nsp1. We have combined results from computed models of nsp1, with
deep mining of all existing protein structures (using PDBMine), and binding
site recognition (using msTALI) to examine the two sites consisting of residues
55-59 and 73-80. Based on our preliminary results, we conclude that the
residues 73-80 appear as the regions that facilitate the critical initial steps
in the function of nsp1. Given the 90% sequence identity between nsp1 from
SARS-CoV-1 and SARS-CoV-2, we conjecture the same critical initiation step in
the function of COVID-19 nsp1.
