NNP

NNP Partners

Publications

1. Srivastava, A. (2025). Emerging paradigms in the lateral and transverse organization in biological membrane and their functional implications: Connecting the dots with biomolecular simulations. Current Opinion in Structural Biology, 94, 103128. https://doi.org/10.1016/j.sbi.2025.103128

2. Mallick, Argha Mario, Ananya Chatterjee, Arun Bahadur Gurung, Prithviraj Uttarasili, Archana Tripathi, Monjuri Hembram, Anand Srivastava, and Rituparna Sinha Roy. "Designed gramicidin-inspired stabilized peptide-based therapeutics to potentiate immunotherapy against aggressive kidney cancer." Biomaterials Science (2025). https://doi.org/10.1039/d5bm00109a

3. Chakraborty, A., Srimali, S., Topno, R., Ranshur, A., & Madhusudhan, M. S. (2025). MAGNETIC: a web server to fetch gene network based on motif distribution in promoters. Nucleic Acids Research, gkaf420. https://doi.org/10.1093/nar/gkaf420

4. Zhang, Y., Jindal, M., Viswanath, S., & Sitharam, M. (2025). A New Discrete-Geometry Approach for Integrative Docking of Proteins Using Chemical Cross-Links. Journal of Chemical Information and Modeling, 65(9), 4576-4592. https://pubs.acs.org/doi/full/10.1021/acs.jcim.4c02412

5. SureshKumar, H., Iyer, S. S., Banerjee, A., Poduval, P., Lyman, E., & Srivastava, A. (2025). Signatures of glassy dynamics in highly ordered lipid bilayers with emergence of soft dynamic channels. The Journal of Chemical Physics, 162(14). https://doi.org/10.1063/5.0250190

6. Balasubramanian, S., Roy, I., Appadurai, R., & Srivastava, A. (2025). The ribonucleoprotein hnRNPA1 mediates binding to RNA and DNA telomeric G-quadruplexes through an RGG-rich region. Journal of Biological Chemistry, 301(5). https://doi.org/10.1016/j.jbc.2025.108491

7. Chakraborty, A., Devarajan, A., Kumar, K., CS, R., Madhusudhan, M. S., Ratnaparkhi, G. S., & Kamat, S. S. (2025). Bioinformatics Analysis Identifies Sequence Determinants of Enzymatic Activity for the PHARC-Associated Lipase ABHD12. Biochemistry, 64(8), 1852-1863. https://doi.org/10.1021/acs.biochem.4c00865?urlappend=%3Fref%3DPDF&jav=VoR&rel=cite-as

8. Srivastava, A. (2025). It takes two to tango: The second membrane-binding site in peripheral proteins. Structure, 33(1), 10-12. https://doi.org/10.1016/j.str.2024.12.007

9. Viswanath, S. (2024). AlphaFold opens the doors to deorphanizing secreted proteins. Cell Systems, 15(11), 1000-1001. https://doi.org/10.1016/j.cels.2024.10.010

10. Baratam, K., & Srivastava, A. (2024). SOP-MULTI: A Self-Organized Polymer-Based Coarse-Grained Model for Multidomain and Intrinsically Disordered Proteins with Conformation Ensemble Consistent with Experimental Scattering Data. Journal of Chemical Theory and Computation, 20(22), 10179-10198. https://doi.org/10.1021/acs.jctc.4c00579?urlappend=%3Fref%3DPDF&jav=VoR&rel=cite-as

11. Natarajan, C., & Srivastava, A. (2024). Efficiently determining membrane-bound conformations of peripheral membrane proteins using replica exchange with hybrid tempering. The European Physical Journal Special Topics, 233(21), 3039-3051. https://doi.org/10.1140/epjs/s11734-024-01386-x

12. Majila, K., Arvindekar, S., Jindal, M., & Viswanath, S. (2025). Frontiers in integrative structural modeling of macromolecular assemblies. QRB discovery, 6, e3. https://doi.org/10.1017/qrd.2024.15 

13. Pandey P, Srivastava A. sAMP-VGG16: Force-field assisted image-based deep neural network prediction model for short antimicrobial peptides. Proteins. 2025; 93(1): 372-383. doi:10.1002/prot.26681

14. Pandey, P., & Srivastava, A. (2025). sAMP-VGG16: Force-field assisted image-based deep neural network prediction model for short antimicrobial peptides. Proteins, 93(1), 372–383. https://doi.org/10.1002/prot.26681

15. Tripathy, M., & Srivastava, A. (2024). Non-affine deformation analysis and 3D packing defects: A new way to probe membrane heterogeneity in molecular simulations. In Methods in Enzymology (Vol. 701, pp. 541-577). Academic Press. https://doi.org/10.1016/bs.mie.2024.03.011

Pre-print

1. K. Majila, V. Ullanat, and S. Viswanath, A deep learning method for predicting interactions for  intrinsically disordered regions of proteins, biorxiv, 2024. https://doi.org/10.1101/2024.12.19.629373

2. Trung, T, Vinothkumar, K.R., Subramanian, R. Cryo-Electron Microscopy in the study of Protein Protein Interactions (book chapter – in review).

Patent

Sinha Roy R., Srivastava A., Mallick A. M., Chatterjee A., Gurung A. B., Uttarasili P., Tripathi A., Hembram M. Indian Institute of Science Education and Research Kolkata. Pharmaceutical Composition for Treatment of Kidney Cancer. Indian patent application no. 202533004009 (patent of addition to granted Indian patent number – 444719). 2025 Jan 17. [In this work, we have looked at the membrane interaction of a gramicidin-inspired designed peptide and will extend the idea to AMPs]