1. Vidhi Sajnani, Omer Ali, Satarupa Das, and Debashree Bandyopadhyay, Identification of Protein–Protein Interaction (PPI) Sites on the Influenza A (H1N1) Viral Genome Using Gradient Boosting and Artificial Neural Network (ANN) Models, ACS Omega 2025, 10, 45, 54185-54199, DOI: 10.1021/acsomega.5c06314 2. Sharayu Ghodeswar and Debashree Bandyopadhyay, ROSBASE1.0: a comprehensive database of reactive oxygen species (ROS): categorization of cell organelles, proteins, taxonomy, and diseases based on ROS-related activities, Database, Volume 2025, 2025, baaf069, https://doi.org/10.1093/database/baaf069 3. Safdari A, Keshav CS, Mody D, Verma K,, Kaushal U, Burra VK, et al. (2025) The external validity of machine learning-based prediction scores from hematological parameters of COVID- 19: A study using hospital records from Brazil, Italy, and Western Europe. PLoS ONE 20(2): e0316467. https://doi.org/10.1371/journal. pone.0316467 4. Lubna, S., & Bandyopadhyay, D. (2024). Consortium of ‘consistent amino acid substitutions’ on influenza A (H1N1) viral proteins emerged at specific stages of viral infection: a big data analysis. Journal of Biomolecular Structure and Dynamics, 1–14. https://doi.org/10.1080/07391102.2024.2435056 5. Structural and mechanistic insights into Quinolone Synthase to address its functional promiscuity May 2024Communications Biology 7(1) DOI: 10.1038/s42003-024-06152-2 Mallika VijayanathanMallika VijayanathanAbhinav Koyamangalath VadakkepatKozhinjampara R. Mahendran, .. Debashree Bandyopadhyay, Radhakrishna Pillai, Soniya e V 6. Diptiman D, Jalan A, Pal R, Dodwani, S, Bandyopadhyay, D, Hist-i-fy—a multiple histidine post-translational-modification (PTM) prediction server based on protein sequences using convolution neural network: a case study on mass spectroscopy data; Journal of Biomolecular Structure and Dynamics; 2024; https://doi.org/10.1080/07391102.2024.2310200 7. Syeda Lubna, Suma Chinta, Prakruthi Burra, Kiranmayi Vedantham, Sibnath Ray, and Debashree Bandyopadhyay, “New substitutions on NS1 protein from influenza A (H1N1) virus: Bioinformatics analyses of Indian strains isolated from 2009 to 2020”, Health Sci. Rep. 2022; 5:e626, doi: https://doi.org/10.1002/hsr2.626 8. Sharayu G, Adrija A Dutta, Shubhomay Panda and Debashree Bandyopadhyay "Computation of free energy changes based on changes in protein microenvironments during first order/pseudo-first order biochemical reactions: Concept tested on ligand/drug binding to SARS-COV2 proteins" (manuscript under preparation) 9. Vamsi Nallapareddy, Shubham Rajendra Bogam, Himaja Debrakonda, Shubham Paliwal and Debashree Bandyopadhyay, “DeepCys: structure-based multiple cysteine function prediction method trained on deep neural network: case study on Domains of Unknown Functions (DUFs) belonging to COX2 domains" Proteins: Structure Function and Bioinformatics 2021; 89, 745-761 DOI: 10.1002/prot.26056 10. Debashree Bandyopadhyay, Akshay Bhatnagar, Shobhit Jain and Prabhav Pratyaksh, “Selective stabilization of aspartic acid protonation state within a given protein conformation occurs via specific ‘molecular association’” J. Phys. Chem. B. 2020, 124, 5350-5361, https://dx.doi.org/10.1021/acs.jpcb.0c02629 11. Aditya, A. Kalyani, S. Singh, M. Bandyopadhyay, D. and Naga Mohan, K., CalPen (Calculator of Penetrance), a web-based tool for estimation of penetrance in genetic studies of complex disorders POLS ONE (2020), 15(1): e0228156, https://doi.org/10.1371/journal.pone.0228156; 12. Akshay Bhatnagar and Debashree Bandyopadhyay, “Characterization of cysteine thiol modifications based on protein microenvironments and local secondary structures”, Proteins; Structure, Function and Bioinformatics (2018), 86(2), 192-209 DOI:10.1002/prot.25424, 13. Akshay Bhatnagar and Debashree Bandyopadhyay, “Cover image”, Proteins: Structure Function and Bioinformatics (2018) 86 (2) pages: C1, DOI:10.1002/prot.25447, 14. Akshay Bhatnagar, Marcin Apostol, Debashree Bandyopadhyay "Amino acid function relates to its embedded protein microenvironment: A study on disulphide-bridged cystine", Proteins: Structure Function Bioinformatics (2016) 84, 1576-1589 15. Sheik saleem Pasha; Pradip Das; Nigam P. Rath; Debashree Bandyopadhyay; Nikhil R. Jana, Inamur R. Laskar, "Water Soluble Luminescent Cyclometalated Platinum(II) Complex - A Suitable Probe for Bio-imaging Applications", Inorganic. Chemistry Communication (2016), 67, 107-111 16. Sheik Saleem Pasha, Parvej Alam, Subhra Dash, Gurpreet Kaur, Debashree Bandyopadhyay, Rajdeep Chowdhury, , Nigam Rath, Angshuman Roy Choudhury, Inamur R. Laskar, "Rare Observation of ‘Aggregation Induced Emission’ in Cyclometalated Platinum(II) Complexes and their Biological Activities”, RSC Advances, (2014), 4, 50549-50553, DOI: 10.1039/C4RA06623E 17. Parvej Alam, Maheswararao Karanam, Debashree Bandyopadhyay, Angshuman Roy Choudhury, Inamur Rahaman Laskar, “Luminescence Vapochromic Properties in a New Class of Aggregation Induced Emission Active Iridium(III)-Diimine Complexes”, European Journal of Inorganic Chemistry, European Journal of Inorganic Chemistry; (2014) 23, 3710-3719, DOI:10.1002/ejic.201402222 18. Akshay Bhatnagar and Debashree Bandyopadhyay, “Role of Microenvironment in modulating structure and function of Cystine residues in high-resolution protein cyrstal structures”, Proceedings of 4th Annual International Conference on Advances in Biotechnology 2014, pages 35-40. 19. Panigrahi, S., Bhattacharya, A., Bandyopadhyay, D., Bhattacharyya, D., Grabowski, S and Banerjee, S., “Wetting Property of the edges of monoatomic step on graphite: Frictional-Force Microscopy and ab initio Quantum Chemical Studies”, J. Phys. Chem C, 2011, 115, 14819-14826 20. Bandyopadhyay, D . Bortolato, A. Mehler, E.L. and Filizola, M. “Improving ab initio long loop predictions in GPCR proteins”, Biophys J, 2008; 94(2), Suppl. 1, pages 664-665 21. Bandyopadhyay, D. and Mehler, E.L., “Quantitative Expression of Protein Heterogeneity: Response of Amino Acid Side Chains to Their Local Environment”, Proteins: Structure, Function and Bioinformatics, 2008; 72(2):646-59 22. Bandyopadhyay, D. and Mehler, E.L., “Formation of precursor to amyloid protein aggregation in the tau fragment 306VQIVYK311”, Biophys J, 224A-224A Suppl. S Jan 2007 23. Bandyopadhyay, D. and Bhattacharyya, D., (2006) “Estimation of Strength in different Extra WatsonCrick Hydrogen Bonds in DNA Double Helices through Quantum chemical studies”, Biopolymers, 83, 313-325. 24. Bandyopadhyay, D. and Bhattacharyya, D., (2003) “Different Modes of Interaction between Hydrated Magnesium Ion and DNA Functional Groups: Database Analysis and ab initio Studies”, J.Biomol.Struct.Dynam. 21, 447-458, 25. Bandyopadhyay, D ., and Bhattacharyya, D., (2002) "Effect of Flanking residues on CA and AA dinucleotides: Some Rationale" J. Biomol. Struct. Dynam. 19, 659-667 26. Bandyopadhyay, D. , and Bhattacharyya, D., (2000) "Effect of Neighboring Bases on Stacking Orientation: A molecular dynamics study" J. Biomol. Struct. Dynam. 18, 29-43

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