Advances in Protein Molecular and Structural Biology Methods

<p>Section I: Techniques to optimize recombinant protein expression in bacteria, yeast, insect, and mammalian cells<br>1. Strategies to Improve the Expression and Solubility of Recombinant Proteins in Bacteria<br>Niharika Nag, Heena Khan, and Timir Tripathi<br>2. Advances in Heterologous Protein Expression Strategies in Yeast and Insect Systems<br>Meenakshi Singh, Smita Gupta, Arun Kumar Rawat, Sudhir Kumar Singh<br>3. Methods for Transient Expression and Purification of Monoclonal Antibodies in Mammalian Cells<br>Suchitra Kamle, Dawei Li, Chun Geun Lee, Jack A. Elias<br>4. Methods for Recombinant Production and Purification of Intrinsically Disordered Proteins<br>Steffen P. Graether</p> <p>Section 2: Biophysical techniques including, NMR, X-ray crystallography, cryo-EM, etc.<br>5. Methods to Determine the Oligomeric Structure of Proteins<br>Purna Bahadur Chetri, Heena Khan, and Timir Tripathi<br>6. Multimodal Methods to Study Protein Aggregation and Fibrillation<br>Maria Georgina Herrera, Marco Giampà, Nicolo Tonali　and Veronica Isabel Dodero<br>7. Experimental Methods to Study the Thermodynamics of Protein-Protein Interactions<br>Santanu Sasidharan, Niharika Nag, Timir Tripathi, and Prakash Saudagar<br>8. Experimental Methods to Study the Kinetics of Protein-Protein Interactions<br>Abhay Narayan Singh, Kristijan Ramadan, Shalini Singh<br>9. Computational Techniques to Study Protein-Protein Interactions <br>Khattab Al-Khafaji, Tugba Taskin-Tok<br>10. Experimental Methods to Study Protein-Nucleic Acid Interactions<br>Roberto Giambruno, Jakob Rupert, and Elsa Zacco<br>11. Advanced Computational Tools for Quantitative Analysis of Protein-nucleic acid Interfaces<br>Sunandan Mukherjee and Chandran Nithin<br>12. Experimental Techniques to Study Protein Dynamics and Conformations<br>Akshita Gupta, Anamika Singh, Nabeel Ahmad, Tej P. Singh, Sujata Sharma, Pradeep Sharma<br>13. Computational Techniques to Study Protein Dynamics and Conformations <br>Laura Orellana, Anil Mhashal, and Agusti Emperador<br>14. Application of Circular Dichroism Spectroscopy in Studying Protein Folding, Stability, and Interaction<br>Md. Anzarul Haque, Punit Kaur, Asimul Islam, and Md. Imtaiyaz Hassan<br>15. Studying Protein Folding Dynamics using Single Molecule Fluorescence Methods<br>Narattam Mandal, Krishnananda Chattopadhyay, Achinta Sannigrahi<br>16. Advances in Liquid-state NMR Spectroscopy to Study the Structure, Function, and Dynamics of Biomacromolecules<br>Priyanka Aggarwal, Pooja Kumari and Neel Sarovar Bhavesh<br>17. In-Cell NMR Spectroscopy: A Tool for Cellular Structure Biology<br>Vijay Kumar<br>18. Current Trends in Membrane Protein Crystallography<br>Koomity V. Nageswar, Mansi Sharma, Dipak N. Patil, Santoshi Nayak, Anwesha Roy, Appu K. Singh<br>19. Advances in Sample Preparation and Data Processing for Single-particle Cryo-Electron Microscopy<br>Anshul Assaiya, Suparna Bhar and Janesh Kumar<br>20. Advanced Mass Spectrometry-Based Approaches for Molecular-Structural Biologists <br>Joanna Bons, Jacob Rose, Amy O’Broin, and Birgit Schilling<br>21. Developments, Advancements, and Contributions of Mass Spectrometry in Omics Technologies<br>Saravanan Kumar<br>22. Role of Structural Biology Methods in Drug Discovery<br>Fouzia Nasim and Insaf Ahmed Qureshi</p> <p>Section 3: Computational methods including MD simulation, coupling MD and deep machine learning, etc<br>23. Prediction, Validation, and Analysis of Protein Structures: A Beginner’s Guide<br>Santanu Sasidharan and Prakash Saudagar<br>24. Advances in Structure-Based Virtual Screening for Drug Discovery<br>Olujide O. Olubiyi, Suman Samantray and Alexander-Maurice Illig<br>25. Methods and Applications of Machine Learning in Structure-Based Drug Discovery<br>Madhumathi Sanjeevi, Prajna N Hebbar, Natarajan Aiswarya, Rashmi S., Chandrasekar Narayanan Rahul, Ajitha Mohan, Jeyaraman Jeyakanthan and Kanagaraj Sekar<br>26. Molecular Dynamics Simulations: Principles, Methods, and Applications in Protein Conformational Dynamics <br>Aditya K. Padhi, Matej Janezic, Kam Y. J. Zhang<br>27. Applications of Molecular Dynamics Simulations in Drug Discovery<br>Xubo Lin<br>28. Envisaging the Conformational Space of Proteins by Coupling Machine Learning and Molecular Dynamics<br>Murali Aarthy, Sanjeev Kumar Singh<br>29. Immunoinformatics and Reverse Vaccinology Methods to Design Peptide-based Vaccines<br>Vinita Sharma, Satyendra Singh, Tadi Sai Ratnakar, Vijay Kumar Prajapati</p> <p>Section 4: Tools and techniques to study IDPs<br>30. Computational Methods to Study Intrinsically Disordered Proteins<br>Prateek Kumar, Aparna Bhardwaj, Vladimir N. Uversky, Timir Tripathi, and Rajanish Giri<br>31. Experimental Methods to Study Intrinsically Disordered Proteins<br>Niharika Nag, Purna B Chetri, Vladimir N. Uversky, Rajanish Giri, and Timir Tripathi<br>32. Analysis of Structure and Dynamics of Intrinsically Disordered Regions in Proteins using Solution NMR Methods<br>Nikita V Saibo, Snigdha Maiti, Bidisha Acharya, and Soumya De<br>33. Methods to Study the Effect of Solution Variables on the Conformational Dynamics of IDPs<br>Hakan Alıcı, Orkun Hasekioglu, Vladimir N. Uversky, and Orkid Coskuner-Weber<br>34. Molecular Simulations to Study IDP-IDP Interactions and Their Complexes<br>Kota Kasahara</p> <p>Section 5: Protein interaction networks, signaling, engineering, and function, etc.<br>35. Exploring Large-Scale Protein Function using Systematic Mutant Analysis<br>Amrita Arpita Padhy, Subhashree Sahoo, Shivani Kumari, Varsha Kumari, Parul Mishra<br>36. Approaches and Methods to Study Cell Signaling: Linguistics of Cellular Communication<br>Siddharth Neog and Vishal Trivedi<br>37. Methods to Study Systems Biology of Signaling Networks: A Case Study of NSCLC<br>Nikhil H. Samarth and Shailza Singh<br>38. Advancements in the Analysis of Protein Post-Translational Modifications<br>Sandip Mukherjee, Ritesh Kumar, Arianne L. Theiss, and K. Venuprasad<br>39. Protein Engineering: Methods and Applications<br>Saurabh Bansal and Bishwajit Kundu<br>40. Designer 3D-DNA Nanodevices: Structures, Functions and Cellular Applications<br>Kahkashan Bansal, Anjali Rajwar, and Dhiraj Bhatia</p>