Computational mutagenesis at the SARS-CoV-2 spike protein/angiotensin-converting enzyme 2 binding interface: comparison with experimental evidence

E Laurini, D Marson, S Aulic, A Fermeglia, S Pricl - ACS nano, 2021 - ACS Publications
… Change in binding free energy predicted by computational mutagenesis of the S-RBD
CoV-2 residues N487 (A), Y489 (B), and Y505 (C) for the corresponding ACE2/S-RBD CoV-2

Identification and computational analysis of mutations in SARS-CoV-2

T Dey, S Chatterjee, S Manna, A Nandy… - Computers in biology and …, 2021 - Elsevier
… of mutation and for single point mutation we … mutation which can be essential to locate
mutations. This study helps us to identify the significant mutations in the proteins of SARS-CoV-2

Omicron and Delta variant of SARSCoV2: a comparative computational study of spike protein

S Kumar, TS Thambiraja, K Karuppanan… - Journal of medical …, 2022 - Wiley Online Library
… binding affinity of SARS-CoV-2 Delta and Omicron variants with ACE2 by using a variety of
computational tools to … The mutation changes of SARS-CoV-2 were predicted using varsite. …

Computational saturation mutagenesis of SARS-CoV-1 spike glycoprotein: Stability, binding affinity, and comparison with SARS-CoV-2

A Sobitan, V Mahase, R Rhoades… - Frontiers in Molecular …, 2021 - frontiersin.org
computational mutagenesis to analyze the effects of missense mutations on the stability
and protein-protein interactions of SARS-CoV-1. … design therapeutic drugs against SARS-CoV-1. …

Molecular dynamics and in silico mutagenesis on the reversible inhibitor-bound SARS-CoV-2 main protease complexes reveal the role of lateral pocket in enhancing …

YL Weng, SR Naik, N Dingelstad, MR Lugo… - Scientific Reports, 2021 - nature.com
… in this pocket through computational mutagenesis. Thus, … computational mutagenesis
analyses demonstrate the importance of HIS163 and its role in ligand engagement in SARS-CoV-2

Computational prediction of mutational effects on SARS-CoV-2 binding by relative free energy calculations

J Zou, J Yin, L Fang, M Yang, T Wang… - Journal of chemical …, 2020 - ACS Publications
… Here we present our results of alanine scanning mutagenesis of SARS-CoV and SARS-CoV-2
S RBD complexed with ACE2 using thermodynamic integration (TI). (21) The hot spot …

Computationally designed ACE2 decoy receptor binds SARS-CoV-2 spike (S) protein with tight nanomolar affinity

B Havranek, KK Chan, A Wu, E Procko… - Journal of chemical …, 2021 - ACS Publications
… Even with the availability of vaccines, therapeutic options for COVID-19 still remain highly …
neutralizes SARS CoV-2 infection by acting as a decoy. Using computational mutagenesis, we …

Computational analysis of dynamic allostery and control in the SARS-CoV-2 main protease

I Dubanevics, TCB McLeish - Journal of the Royal …, 2021 - royalsocietypublishing.org
… Furthermore, the experimentally identified residue N214 is signposted by these calculations:
its computational mutation generates the largest fluctuation free energy change upon spring …

Computational decomposition reveals reshaping of the SARSCoV2–ACE2 interface among viral variants expressing the N501Y mutation

E Socher, M Conrad, L Heger, F Paulsen… - Journal of cellular …, 2021 - Wiley Online Library
computational decomposition of the RBD–ACE2 interface can identify residues on the RBD
that are critical for virus–host interactions across different SARS-CoV-2two sites of mutation

Computational analysis of mutations in the receptor-binding domain of sars-cov-2 spike and their effects on antibody binding

ME Bozdaganyan, KV Shaitan, MP Kirpichnikov… - Viruses, 2022 - mdpi.com
… a comprehensive computational investigation of … mutagenesis analysis reported here
will guide further experimental studies of Ab resistance and identification of natural SARS-CoV-2