Dedication
Contents
Contributors
About the Editors
Foreword • Amit Sharma
Preface
1. Strategies to improve the expression and solubility of recombinant proteins in E. coli • Niharika Nag, Heena Khan, and Timir Tripathi
2. Advances in heterologous protein expression strategies in yeast and insect systems • Meenakshi Singh, Smita Gupta, Arun Kumar Rawat, and Sudhir Kumar Singh
3. Methods for transient expression and purification of monoclonal antibodies in mammalian cells • Suchitra Kamle, Dawei Li, Chun Geun Lee, and Jack A. Elias
4. Methods for recombinant production and purification of intrinsically disordered proteins • Steffen P. Graether
5. Methods to determine the oligomeric structure of proteins • Purna Bahadur Chetri, Heena Khan, and Timir Tripathi
6. Multimodal methods to study protein aggregation and fibrillation • Maria Georgina Herrera, Marco Giampà, Nicolo Tonali, and Veronica Isabel Dodero
7. Experimental methods to study the thermodynamics of protein–protein interactions • Santanu Sasidharan, Niharika Nag, Timir Tripathi, and Prakash Saudagar
8. Experimental methods to studythe kinetics of protein–protein interactions • Abhay Narayan Singh, Kristijan Ramadan, and Shalini Singh
9. Computational techniques for studying protein-protein interactions • Khattab Al-Khafaji and Tugba Taskin-Tok
10. Experimental methods to study protein–nucleic acid interactions • Roberto Giambruno, Jakob Rupert, and Elsa Zacco
11. Advanced computational tools for quantitative analysis of protein–nucleicacid interfaces • Sunandan Mukherjee and Chandran Nithin
12. Experimental techniques to study protein dynamics and conformations • Akshita Gupta, Anamika Singh, Nabeel Ahmad, Tej P. Singh, Sujata Sharma, and Pradeep Sharma
13. Computational techniques to study protein dynamics and conformations • Anil Mhashal, Agusti Emperador, and Laura Orellana
14. Application of circular dichroism spectroscopy in studying protein folding, stability, and interaction • Md Anzarul Haque, Punit Kaur, Asimul Islam, and Md Imtaiyaz Hassan
15. Studying protein-folding dynamics using single-molecule fluorescence methods • Narattam Mandal, Krishnananda Chattopadhyay, and Achinta Sannigrahi
16. Advances in liquid-state NMR spectroscopy to study the structure, function, and dynamics of biomacromolecules • Priyanka Aggarwal, Pooja Kumari, and Neel Sarovar Bhavesh
17. In-cell NMR spectroscopy: A tool to study cellular structure biology • Vijay Kumar
18. Current trends in membrane protein crystallography • Koomity V. Nageswar, Mansi Sharma, Dipak N. Patil, Santoshi Nayak, Anwesha Roy, and Appu K. Singh
19. Advances in sample preparation and data processing for single-particle cryo-electron microscopy • Anshul Assaiya, Suparna Bhar, and Janesh Kumar
20. Advanced mass spectrometry-based methods for protein molecular-structural biologists • Joanna Bons, Jacob Rose, Amy O’Broin, and Birgit Schilling
21. Developments, advancements, and contributions of mass spectrometry in omics technologies • Saravanan Kumar
22. Role of structural biology methods in drug discovery • Fouzia Nasim and Insaf Ahmed Qureshi
23. Prediction, validation, and analysis of protein structures: A beginner’s guide • Santanu Sasidharan and Prakash Saudagar
24. Advances in structure-based virtual screening for drug discovery • Olujide O. Olubiyi, Suman Samantray, and Alexander-Maurice Illig
25. Methods and applications of machine learning in structure-based drug discovery • Madhumathi Sanjeevi, Prajna N. Hebbar, Natarajan Aiswarya, S. Rashmi, Chandrashekar Narayanan Rahul, Ajitha Mohan, Jeyaraman Jeyakanthan, and Kanagaraj Sekar
26. Molecular dynamics simulations: Principles, methods, and applications in protein conformational dynamics • Aditya K. Padhi, Matej Janežic, and Kam Y.J. Zhang
27. Applications of molecular dynamics simulations in drug discovery • Xubo Lin
28. Envisaging the conformational space of proteins by coupling machine learning and molecular dynamics • Murali Aarthy and Sanjeev Kumar Singh
29. Immunoinformatics and reverse vaccinology methods to design peptide-based vaccines • Vinita Sharma, Satyendra Singh, Tadi Sai Ratnakar, and Vijay Kumar Prajapati
30. Computational methods to study intrinsically disordered proteins • Prateek Kumar, Aparna Bhardwaj, Vladimir N. Uversky, Timir Tripathi, and Rajanish Giri
31. Experimental methods to study intrinsically disordered proteins • Niharika Nag, Purna Bahadur Chetri, Vladimir N. Uversky, Rajanish Giri, and Timir Tripathi
32. Analysis of structure and dynamics of intrinsically disordered regions in proteins using solution NMR methods • Nikita V. Saibo, Snigdha Maiti, Bidisha Acharya, and Soumya De
33. Methods to study the effect of solution variables on the conformational dynamics of intrinsically disordered proteins • Hakan Alici, Orkun Hasekioglu, Vladimir N. Uversky, and Orkid Coskuner-Weber
34. Molecular simulations to study IDP-IDP interactions and their complexes • Kota Kasahara
35. Exploring large-scale protein function using systematic mutant analysis • Amrita Arpita Padhy, Subhashree Sahoo, Kummari Shivani, Varsha Kumari, and Parul Mishra
36. Approaches and methods to study cell signaling: Linguistics of cellular communication • Siddharth Neog and Vishal Trivedi
37. Methods to study systems biology of signaling networks: A case study of NSCLC • Nikhil H. Samarth and Shailza Singh
38. Advancements in the analysis of protein post-translational modifications • Sandip Mukherjee, Ritesh Kumar, Arianne L. Theiss, and K. Venuprasad
39. Protein engineering: Methods and applications • Saurabh Bansal and Bishwajit Kundu
40. Designer 3D-DNA nanodevices: Structures, functions, and cellular applications • Anjali Rajwar, Payal Vaswani, A. Hema Naveena, and Dhiraj Bhatia
Index