In Silico Modeling of Drugs Against Coronaviruses: Computational Tools and Protocols
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Section I: Introduction
1. History and Recent Advances in Coronavirus Discovery
Sora Abdul-Fattah, Aman Pal, Nagham Kaka, and Pramath Kakodkar
2. The Origin, Transmission, and Clinical Therapies in the Management of Coronavirus Diseases
Nagham Kaka, Aman Pal, Sora Abdul-Fattah, and Pramath Kakodkar
3. Transmission, Medical Consequences, and Prevention/Treatment of COVID-19 Infection
Suliman Khan, Rabeea Siddique, and Aigerim Bizhanova
4. Molecular-Level Targets for Development of Therapies Against Coronavirus Diseases
Qiongqiong Angela Zhou, Roger Granet, and Linda V. Garner
5. Candidate Drugs for the Potential Treatment of Coronavirus Diseases
Thanigaimalai Pillaiyar, Manoj Manickam, Sangeetha Meenakshisundaram, and Ajith Jerome Benjamine
Section II: Tools and Methodologies
6. Ligand-Based Approaches for Development of Drugs Against SARS-CoV-2
Ekampreet Singh, Rameez Jabeer Khan, Rajat Kumar Jha, Gizachew Muluneh Amera, Monika Jain, Rashmi Prabha Singh, Jayaraman Muthukumaran, and Amit Kumar Singh
7. Computational Drug Repurposing for Development of Drugs Against Coronaviruses
Ekampreet Singh, Rameez Jabeer Khan, Rajat Kumar Jha, Gizachew Muluneh Amera, Monika Jain, Rashmi Prabha Singh, Jayaraman Muthukumaran, and Amit Kumar Singh
8. Computational Methods and Tools for Repurposing of Drugs Against Coronaviruses
Sohini Chakraborti, Sneha Bheemireddy, and Narayanaswamy Srinivasan
9. Molecular Multi-Target Approach on COVID-19 for Designing Novel Chemicals
Pawan Kumar and Indira Ghosh
10. Structural Bioinformatics to Unveil Weaknesses of Coronavirus Spike Glycoprotein Stability
Pietro Bongini, Alfonso Trezza, Monica Bianchini, Ottavia Spiga, and Neri Niccolai
11. Protein-Protein Interaction Network for Identification of New Targets Against Novel Coronavirus
Suresh Kumar
12. Nonequilibrium Alchemical Simulations for the Development of Drugs Against COVID-19
Marina Macchiagodena, Maurice Karrenbrock, Marco Pagliai, Guido Guarnieri, Francesco Iannone, and Piero Procacci
13. Therapeutic and Vaccine Strategies for Stopping the COVID-19 Pandemic Based on Structural and Molecular Modelling Studies of Virus-Ganglioside Interactions
Jacques Fantini
14. Discovery of Covalent Drugs Targeting the Key Enzymes of SARS-CoV-2 Using SCARdock
Qi Song, Zhiying Wang, and Sen Liu
15. Machine Learning Techniques for Development of Drugs Against Coronavirus-2019 (COVID-19): A Case Study Protocol
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