Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures

Chapter 1 Papain-Like Cysteine Protease (PLpro)

Chapter 2 3C-Like Protease (3CLpro)

Chapter 3 RNA-Dependent RNA Polymerase (RdRp)

Chapter 4 RNA Helicase

Chapter 5 RNA Helicase Binding with RdRp, NSP7, NSP8a, NSP8b, pRNA, tRNA, ADP-Mg 2 + $$\text{ADP-Mg}^{2+}$$ , and ATP-Mg 2 + $$\text{ATP-Mg}^{2+}$$

Chapter 6 RNA Helicase Binding with ADP-Mg 2 + $$\text{ADP-Mg}^{2+}$$ , ATP-Mg 2 + $$\text{ATP-Mg}^{2+}$$ , and RNA

Chapter 7 Spike (S) Glycoprotein

Chapter 8 Spike (S) Glycoprotein D614G Mutant

Chapter 9 Spike (S) Glycoprotein N501Y Mutant

Chapter 10 Spike (S) Glycoprotein N165A and N234A Mutant

Chapter 11 SARS (SARS-CoV-1)

Chapter 12 MERS-Coronavirus (MERS)

Chapter 13 Human ACE2, Human IL6, Human IL6R, and Human nAChRs

Chapter 15 3CLpro Binding with N3/Lopinavir/Ritonavir

Chapter 16 3CLpro Dimer Binding with 7 HIV Inhibitors and Others

Chapter 17 Spike RBDs Binding with 50 Drugs

Chapter 18 Human ACE2 Ectodomain Binding with 78 Drugs

Chapter 19 Spike-and-ACE2 Binding with 100 Drugs

Chapter 20 Envelope Protein (E-Protein)

Chapter 21 Membrane Glycoprotein (M-Protein)

Chapter 22 Nucleocapsid Phosphoprotein (N-Protein)

Chapter 23 SARS-CoV-2 RNA Genome

Chapter 24 NSP7, NSP8, NSP9, NSP10, NSP16, and NSP14

Chapter 25 NSP15

Chapter 26 Other Mutants

Chapter 27 Vaccines and Drugs

Chapter 28 Pandemic Mathematical Models, Epidemiology, and Virus Origins