MutCov is a user-friendly pipeline for evaluating the effect of mutations in spike protein on SARS-CoV-2
infectivity and antigenicity by calculating the binding free energy between spike protein and angiotensin
converting enzyme 2 (ACE2) or neutralizing monoclonal antibodies.
MutCov takes amino acid change in S protein as input to predict the infectivity and antigenicity of mutant
SARS-CoV-2 through four main analytical modules based on state-of-the-art computational tools:
• homology modeling of mutant S protein using MODELLER
• mutant S protein docking to its receptor (ACE2 or NAb) using PyMOL
• molecular dynamics (MD) simulations of the infection or neutralization process of wildtype and mutant SARS-CoV-2 using Gromacs
• binding free energy calculations of S protein with hACE2 or NAbs using the g_mmpbsa