1. Singhal, T. A Review of Coronavirus Disease-2019 (COVID-19). Indian Journal of Pediatrics vol. 87 281–286 (2020).
2. Roy, B. & Roy, H. The Delta Plus variant of COVID-19: Will it be the worst nightmare in the SARS-CoV-2 pandemic? Journal of Biomedical Sciences 8, 1–2 (2021).
3. Khan, A. et al. Higher infectivity of the SARS-CoV-2 new variants is associated with K417N/T, E484K, and N501Y mutants: An insight from structural data. Journal of Cellular Physiology (2021) doi:10.1002/jcp.30367.
4. Kupferschmidt, K. & Wadman, M. Delta variant triggers new phase in the pandemic. Science 372, 1375–1376 (2021).
5. Durmaz, B., Abdulmajed, O. & Durmaz, R. Mutations observed in the SARS-CoV-2 spike glycoprotein and their effects in the interaction of virus with ACE-2 receptor. Medeniyet Medical Journal 35, 253–260 (2020).
6. dos Santos, W. G. Impact of virus genetic variability and host immunity for the success of COVID-19 vaccines. Biomedicine and Pharmacotherapy vol. 136 (2021).
7. Yao, H. et al. Rational development of a human antibody cocktail that deploys multiple functions to confer Pan-SARS-CoVs protection. Cell Research 31, 25–36 (2021).
8. Fatihi, S. et al. A rigorous framework for detecting SARS-CoV-2 spike protein mutational ensemble from genomic and structural features. doi:10.1101/2021.02.17.431625.
9. Yuan, M. et al. A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV. http://science.sciencemag.org/.
10. Wu, Y. et al. A noncompeting pair of human neutralizing antibodies block COVID-19 virus binding to its receptor ACE2 Downloaded from. http://science.sciencemag.org/ (2021).
11. Shi, R. et al. A human neutralizing antibody targets the receptor-binding site of SARS-CoV-2. Nature 584, 120–124 (2020).
12. Ju, B. et al. Human neutralizing antibodies elicited by SARS-CoV-2 infection. Nature 584, 115–119 (2020).
13. Hansen, J. et al. Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail. http://science.sciencemag.org/.
14. Cao, Y. et al. Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients’ B Cells. Cell 182, 73-84.e16 (2020).
15. Yuan, S., Chan, H. C. S. & Hu, Z. Using PyMOL as a platform for computational drug design. Wiley Interdisciplinary Reviews: Computational Molecular Science 7, e1298 (2017).
16. Choi, Y. & Chan, A. P. PROVEAN web server: A tool to predict the functional effect of amino acid substitutions and indels. Bioinformatics 31, 2745–2747 (2015).
17. Altschup, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. Basic Local Alignment Search Tool. J. Mol. Biol vol. 215 (1990).
18. Venselaar, H., te Beek, T. A. H., Kuipers, R. K. P., Hekkelman, M. L. & Vriend, G. Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinformatics 11, (2010).
19. Kuriata, A. et al. CABS-flex 2.0: A web server for fast simulations of flexibility of protein structures. Nucleic Acids Research 46, W338–W343 (2018).
20. Pettersen, E. F. et al. UCSF Chimera - A visualization system for exploratory research and analysis. Journal of Computational Chemistry 25, 1605–1612 (2004).
21. Brenke, R. et al. Application of asymmetric statistical potentials to antibody-protein docking. Bioinformatics 28, 2608–2614 (2012).
22. Wallace, A. C., Laskowski, R. A. & Thornton, J. M. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions The LIGPLOT program automatically generates schematic 2-D representations of protein-ligand complexes from standard Protein Data Bank file input. Protein Engineering vol. 8 https://academic.oup.com/peds/article-abstract/8/2/127/1561050 (1995).
23. Keretsu, S., Bhujbal, S. P. & Cho, S. J. Rational approach toward COVID-19 main protease inhibitors via molecular docking, molecular dynamics simulation and free energy calculation. Scientific Reports 10, (2020).
24. Tai, W. et al. Characterization of the receptor-binding domain (RBD) of 2019 novel Coronavirus: implication for development of RBD protein as a viral attachment inhibitor and vaccine. Cellular and Molecular Immunology 17, 613–620 (2020).
25. Sironi, M. et al. SARS-CoV-2 and COVID-19: A genetic, epidemiological, and evolutionary perspective. Infection, Genetics and Evolution vol. 84 (2020).
26. Harvey, W. T. et al. SARS-CoV-2 variants, spike mutations and immune escape. Nature Reviews Microbiology vol. 19 409–424 (2021).
27. Dai, L. & Gao, G. F. Viral targets for vaccines against COVID-19. Nature Reviews Immunology vol. 21 73–82 (2021).
28. Liao, M. ling, Somero, G. N. & Dong, Y. wei. Comparing mutagenesis and simulations as tools for identifying functionally important sequence changes for protein thermal adaptation. Proceedings of the National Academy of Sciences of the United States of America 116, 679–688 (2019).
29. Wiedemann, C., Kumar, A., Lang, A. & Ohlenschläger, O. Cysteines and Disulfide Bonds as Structure-Forming Units: Insights From Different Domains of Life and the Potential for Characterization by NMR. Frontiers in Chemistry vol. 8 (2020).
30. MacKerell, A. D. & Nilsson, L. Molecular dynamics simulations of nucleic acid-protein complexes. Current Opinion in Structural Biology vol. 18 194–199 (2008).
31. Carino, A. et al. Hijacking SARS-CoV-2/ACE2 receptor interaction by natural and semi-synthetic steroidal agents acting on functional pockets on the receptor binding domain. Frontiers in Chemistry 8, 1–15 (2020).
32. Shang, J. et al. Structural basis of receptor recognition by SARS-CoV-2. Nature 581, 221–224 (2020).
33. Cerutti, G. et al. Potent SARS-CoV-2 Neutralizing Antibodies Directed Against Spike N-Terminal Domain Target a Single Supersite Lead Contact. doi:10.1101/2021.01.10.426120.
34. Yang, J. et al. Prevalence of comorbidities and its effects in coronavirus disease 2019 patients: A systematic review and meta-analysis. International Journal of Infectious Diseases 94, 91–95 (2020).
35. Ge, J. et al. Antibody neutralization of SARS-CoV-2 through ACE2 receptor mimicry. Nature Communications 12, (2021).
36. Tada, T. et al. Comparison of Neutralizing Antibody Titers Elicited by mRNA and Adenoviral Vector Vaccine against SARS-CoV-2 Variants. bioRxiv 2021.07.19.452771 (2021) doi:10.1101/2021.07.19.452771.