Structural Analysis of SARS-CoV-2 Proteins

The 3D crystal protein-structures of SARS-CoV-2 3CLpro (PDB ID: 6LU7) (Hall and Ji, 2020 (link)), SARS-CoV-2 spike protein-ACE-2 receptor-binding domain (RBD) (PDB ID: 6M17) (Wu et al., 2020 (link)), and human ACE2 (PDB ID: 1R4L) (Joshi et al., 2020 (link)) were obtained from the RCSB PDB database (http://www.rcsb.org/pdb). The 3D crystal structures of SARS-CoV-2 RdRp generated through homology modeling using ICM 3.7.3 modeling software was gifted by Prof. Hua Li, Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (Wu et al., 2020 (link)). The energy minimization of targeted protein structures was performed using the YASARA server. The protein preparation was done with AutoDock Tools Version 1.5.6.