Advances in Protein Molecular and Structural Biology Methods

Dr. Timir Tripathi is a Professor of Molecular Biology, School of Life Sciences, North-Eastern Hill University, Shillong, India. He previously held positions as Regional Director of IGNOU in Kohima and a Senior Assistant Professor in the Department of Biochemistry at NEHU. His research focuses on protein–substrate interactions, conformational dynamics, and the regulatory roles of non-catalytic domains. He is especially interested in intrinsically disordered and phase-separated proteins, their roles in disease, and, more recently, molecular memory, adaptive learning, and intelligence in proteins. Professor Tripathi has received several awards and is an Associate Fellow of the Indian National Science Academy, New Delhi, and an elected member of the National Academy of Sciences, India. He is a section editor of Elsevier's International Journal of Biological Macromolecules and has published five books with Elsevier.Vikash Kumar Dubey is a Professor at the School of Biochemical Engineering and Associate Dean for Academic Affairs at the Indian Institute of Technology (BHU), Varanasi, India. Prior to joining IIT (BHU), he was a postdoctoral fellow at Florida State University, USA before joining IIT Guwahati, India, where he served as Associate Professor and Professor. He has received several awards and has been elected as a member of a number of scientific societies and academies. Among these, he is currently the Vice President of the Bioinformatics and Drug Discovery Society [BIDDS], India and a Fellow of the Royal Society of Biology, UK.

• Section I: Techniques to optimize recombinant protein expression in bacteria, yeast, insect, and mammalian cells1. Strategies to Improve the Expression and Solubility of Recombinant Proteins in BacteriaNiharika Nag, Heena Khan, and Timir Tripathi2. Advances in Heterologous Protein Expression Strategies in Yeast and Insect SystemsMeenakshi Singh, Smita Gupta, Arun Kumar Rawat, Sudhir Kumar Singh3. Methods for Transient Expression and Purification of Monoclonal Antibodies in Mammalian CellsSuchitra Kamle, Dawei Li, Chun Geun Lee, Jack A. Elias4. Methods for Recombinant Production and Purification of Intrinsically Disordered ProteinsSteffen P. GraetherSection 2: Biophysical techniques including, NMR, X-ray crystallography, cryo-EM, etc.5. Methods to Determine the Oligomeric Structure of ProteinsPurna Bahadur Chetri, Heena Khan, and Timir Tripathi6. Multimodal Methods to Study Protein Aggregation and FibrillationMaria Georgina Herrera, Marco Giampà, Nicolo Tonali　and Veronica Isabel Dodero7. Experimental Methods to Study the Thermodynamics of Protein-Protein InteractionsSantanu Sasidharan, Niharika Nag, Timir Tripathi, and Prakash Saudagar8. Experimental Methods to Study the Kinetics of Protein-Protein InteractionsAbhay Narayan Singh, Kristijan Ramadan, Shalini Singh9. Computational Techniques to Study Protein-Protein Interactions Khattab Al-Khafaji, Tugba Taskin-Tok10. Experimental Methods to Study Protein-Nucleic Acid InteractionsRoberto Giambruno, Jakob Rupert, and Elsa Zacco11. Advanced Computational Tools for Quantitative Analysis of Protein-nucleic acid InterfacesSunandan Mukherjee and Chandran Nithin12. Experimental Techniques to Study Protein Dynamics and ConformationsAkshita Gupta, Anamika Singh, Nabeel Ahmad, Tej P. Singh, Sujata Sharma, Pradeep Sharma13. Computational Techniques to Study Protein Dynamics and Conformations Laura Orellana, Anil Mhashal, and Agusti Emperador14. Application of Circular Dichroism Spectroscopy in Studying Protein Folding, Stability, and InteractionMd. Anzarul Haque, Punit Kaur, Asimul Islam, and Md. Imtaiyaz Hassan15. Studying Protein Folding Dynamics using Single Molecule Fluorescence MethodsNarattam Mandal, Krishnananda Chattopadhyay, Achinta Sannigrahi16. Advances in Liquid-state NMR Spectroscopy to Study the Structure, Function, and Dynamics of BiomacromoleculesPriyanka Aggarwal, Pooja Kumari and Neel Sarovar Bhavesh17. In-Cell NMR Spectroscopy: A Tool for Cellular Structure BiologyVijay Kumar18. Current Trends in Membrane Protein CrystallographyKoomity V. Nageswar, Mansi Sharma, Dipak N. Patil, Santoshi Nayak, Anwesha Roy, Appu K. Singh19. Advances in Sample Preparation and Data Processing for Single-particle Cryo-Electron MicroscopyAnshul Assaiya, Suparna Bhar and Janesh Kumar20. Advanced Mass Spectrometry-Based Approaches for Molecular-Structural Biologists Joanna Bons, Jacob Rose, Amy O’Broin, and Birgit Schilling21. Developments, Advancements, and Contributions of Mass Spectrometry in Omics TechnologiesSaravanan Kumar22. Role of Structural Biology Methods in Drug DiscoveryFouzia Nasim and Insaf Ahmed QureshiSection 3: Computational methods including MD simulation, coupling MD and deep machine learning, etc23. Prediction, Validation, and Analysis of Protein Structures: A Beginner’s GuideSantanu Sasidharan and Prakash Saudagar24. Advances in Structure-Based Virtual Screening for Drug DiscoveryOlujide O. Olubiyi, Suman Samantray and Alexander-Maurice Illig25. Methods and Applications of Machine Learning in Structure-Based Drug DiscoveryMadhumathi Sanjeevi, Prajna N Hebbar, Natarajan Aiswarya, Rashmi S., Chandrasekar Narayanan Rahul, Ajitha Mohan, Jeyaraman Jeyakanthan and Kanagaraj Sekar26. Molecular Dynamics Simulations: Principles, Methods, and Applications in Protein Conformational Dynamics Aditya K. Padhi, Matej Janezic, Kam Y. J. Zhang27. Applications of Molecular Dynamics Simulations in Drug DiscoveryXubo Lin28. Envisaging the Conformational Space of Proteins by Coupling Machine Learning and Molecular DynamicsMurali Aarthy, Sanjeev Kumar Singh29. Immunoinformatics and Reverse Vaccinology Methods to Design Peptide-based VaccinesVinita Sharma, Satyendra Singh, Tadi Sai Ratnakar, Vijay Kumar PrajapatiSection 4: Tools and techniques to study IDPs30. Computational Methods to Study Intrinsically Disordered ProteinsPrateek Kumar, Aparna Bhardwaj, Vladimir N. Uversky, Timir Tripathi, and Rajanish Giri31. Experimental Methods to Study Intrinsically Disordered ProteinsNiharika Nag, Purna B Chetri, Vladimir N. Uversky, Rajanish Giri, and Timir Tripathi32. Analysis of Structure and Dynamics of Intrinsically Disordered Regions in Proteins using Solution NMR MethodsNikita V Saibo, Snigdha Maiti, Bidisha Acharya, and Soumya De33. Methods to Study the Effect of Solution Variables on the Conformational Dynamics of IDPsHakan Alıcı, Orkun Hasekioglu, Vladimir N. Uversky, and Orkid Coskuner-Weber34. Molecular Simulations to Study IDP-IDP Interactions and Their ComplexesKota KasaharaSection 5: Protein interaction networks, signaling, engineering, and function, etc.35. Exploring Large-Scale Protein Function using Systematic Mutant AnalysisAmrita Arpita Padhy, Subhashree Sahoo, Shivani Kumari, Varsha Kumari, Parul Mishra36. Approaches and Methods to Study Cell Signaling: Linguistics of Cellular CommunicationSiddharth Neog and Vishal Trivedi37. Methods to Study Systems Biology of Signaling Networks: A Case Study of NSCLCNikhil H. Samarth and Shailza Singh38. Advancements in the Analysis of Protein Post-Translational ModificationsSandip Mukherjee, Ritesh Kumar, Arianne L. Theiss, and K. Venuprasad39. Protein Engineering: Methods and ApplicationsSaurabh Bansal and Bishwajit Kundu40. Designer 3D-DNA Nanodevices: Structures, Functions and Cellular ApplicationsKahkashan Bansal, Anjali Rajwar, and Dhiraj Bhatia