Innovations and Implementations of Computer Aided Drug Discovery Strategies in Rational Drug Design

1. Front Matter

   Pages i-vii

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2. CADD: Some Success Stories from Sanjeevini and the Way Forward

   • Ankita Singh, Shashank Shekhar, B. Jayaram

   Pages 1-18

3. Virtual Screening: Practical Application of Docking, Consensus Scoring and Rescoring Using Binding Free Energy

   • Sunita Gupta, Mohd. Waseem, Naveen Kumar Meena, Roopa Kuntal, Andrew M. Lynn, Smriti Mishra

   Pages 19-33

4. Aspects of Protein Structure, Function, and Dynamics in Rational Drug Designing

   • Daliah Michael, Namrata Bankoti, Ansuman Biswas, K. Sekar

   Pages 35-57

5. Role of Advanced Computing in the Drug Discovery Process

   • Ajitha Mohan, Suparna Banerjee, Kanagaraj Sekar

   Pages 59-90

6. Protein Structure, Dynamics and Assembly: Implications for Drug Discovery

   • Arangasamy Yazhini, Sohini Chakraborti, Narayanaswamy Srinivasan

   Pages 91-122

7. Recent Trends in Computer-Aided Drug Design

   • Seneha Santoshi, Puniti Mathur

   Pages 123-151

8. Predicting Protein Folding and Protein Stability by Molecular Dynamics Simulations for Computational Drug Discovery

   • Ishwar Chandra, Chirasmita Nayak, Sanjeev Kumar Singh

   Pages 153-177

9. Magnitude and Advancements of CADD in Identifying Therapeutic Intervention against Flaviviruses

   • Murali Aarthy, Umesh Panwar, Sanjeev Kumar Singh

   Pages 179-203

10. Elucidating Protein-Ligand Interactions Using High Throughput Biophysical Techniques

    • Nipanshu Agarwal, Vivek Chetry, Krishna Mohan Poluri

    Pages 205-244

11. In Silico Approach in Drug Design and Drug Discovery: An Update

    • Neetu Jabalia, Atul Kumar, Vinit Kumar, Reshma Rani

    Pages 245-271

12. Biological Implications of Polyethylene Glycol and PEGylation: Therapeutic Approaches Based on Biophysical Studies and Protein Structure-Based Drug Design Tools

    • Neha Raina, Amit Kumar Singh, Asimul Islam

    Pages 273-294

13. Molecular Dynamics Simulation in Drug Discovery: Opportunities and Challenges

    • Rohit Shukla, Timir Tripathi

    Pages 295-316

14. Molecular Dynamic Simulation of Intrinsically Disordered Proteins and Relevant Forcefields

    • Prateek Kumar, Nitin Sharma, Amit Kumar, Rajanish Giri

    Pages 317-333

This book presents various computer-aided drug discovery methods for the design and development of ligand and structure-based drug molecules. A wide variety of computational approaches are now being used in various stages of drug discovery and development, as well as in clinical studies. Yet, despite the rapid advances in computer software and hardware, combined with the exponential growth in the available biological information, there are many challenges that still need to be addressed, as this book shows. 


In turn, it shares valuable insights into receptor-ligand interactions in connection with various biological functions and human diseases. The book discusses a wide range of phylogenetic methods and highlights the applications of Molecular Dynamics Simulation in the drug discovery process. It also explores the application of quantum mechanics in order to provide better accuracy when calculating protein-ligand binding interactions and predicting binding affinities. In closing, the book provides illustrative descriptions of major challenges associated with computer-aided drug discovery for the development of therapeutic drugs. Given its scope, it offers a valuable asset for life sciences researchers, medicinal chemists and bioinformaticians looking for the latest information on computer-aided methodologies for drug development, together with their applications in drug discovery.

• Drug Design
• CADD
• Pharmacophore and QSAR
• Molecular Docking
• Molecular Dynamics Simulation
• Rational Drug Design
• Protein Structure
• Protein-Ligand Interactions

• Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India

  Sanjeev Kumar Singh

Dr. Singh is currently Professor at Department of Bioinformatics, Alagappa University, Karaikudi (TN), India. He received his graduation, post graduation and Doctoral degree in Theoretical chemistry from the CSJM University, Kanpur. Before joining Alagappa, he worked as scientist in NIPER, Mohali, Punjab and Assistant Professor, Madurai Kamaraj University, Tamil Nadu.  Prof. Singh possess extensive exposure and achieved a distinct landmark in the area of Drug Discovery and development on specific therapeutic targets of Viruses, Bacterial pathogens and Cancer. He has received “ICMR Lala RAM Chand Kandhari Award and Fellow of BRSI Award”. He is the Secretary General of Bioinformatics and Drug Discovery Society (BIDDS), and MNASc, Member of “The National Academy of Sciences”, India and published more than 130 research articles in highly reputed journals.

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