PUBLICATIONS [Citations: 1209, h-index: 18, i10-index: 22, Total IF = 125.41]
https://scholar.google.co.in/citations?hl=en&user=bJz7GokAAAAJ
DURING SENIOR RESEARCH ASSOCIATESHIP
1. Kumar,R., Borkotoky, S.,Gupta,R., Gupta,J., Maji,S., Tiwari,S.,Tyagi, RK., Oliva, B. (2025). Stabilizing the Shield: C-Terminal Tail Mutation of HMPV F Protein for Enhanced Vaccine Design. BioMedInformatics, 5(3):47. https://doi.org/10.3390/biomedinformatics5030047 (IF: 3.4)
2. Lokshman, M.K., Suhag, K., Kumar, D., Borkotoky, S., Banerjee, M. (2025). A disassembly intermediate of a non-enveloped virus indicates the pathway of genome release. Journal of Molecular Biology, 437(22):169354. https://doi.org/10.1016/j.jmb.2025.169354 (IF: 4.5; Citations: 01)
3. Suhag, K., Borkotoky, S., Siddiqui, S.I., Kumar, J., Kumar, C.S., Tatiya, P., Ghosh, S., Banerjee, M. (2024). Mechanistic Insights into the Divergent Membrane Activities of a Viroporin from Chikungunya Virus and Its Transframe Variant. ACS Infectious Diseases, 11(2) : 430-441, https://doi.org/10.1021/acsinfecdis.4c00562. (IF: 4.1; Citations: 07)
DURING ASSISTANT PROFESSORSHIP
4. Tiwari, H, Ilyas, A, Rai, P.K., Upadhyay,S., and Borkotoky, S. (2025). Computational investigation of antiviral peptide interactions with Mpox DNA polymerase. In Silico Pharmacology. 13 (1), 49. https://doi.org/10.1007/s40203-025-00342-4
5. Tiwari, H, Ilyas, A, Rai, P.K., Upadhyay,S., and Borkotoky, S. (2025). Computational screening of FDA-approved and natural compounds against Mpox Dual specificity protein phosphatase (H1). Indian Journal of Biochemistry and Biophysics. 62 (04): 398-405. https://doi.org/10.56042/ijbb.v62i4.14395 (IF:1.48; Citations: 02)
6. Shrivastav, G., Borkotoky, S., Dey, D., Singh, B., Malhotra, N., Azad, K., Jayaram, B., Agarwal, M., and Banerjee, M. (2023). Structure and energetics guide dynamic behaviour in a T = 3 icosahedral virus capsid. Biophysical Chemistry, 305:107152. https://doi.org/10.1016/j.bpc.2023.107152 (IF:3.8; Citations: 04)
7. Laxman, Borkotoky, S., Saravanan, V., Murali, A. (2023). The application of MD simulation to lead identification, vaccine design, and structural studies in combat against leishmaniasis - A review. Mini-Reviews in Medicinal Chemistry .24(11):1089-1111
http://dx.doi.org/10.2174/1389557523666230901105231 (IF:3.8; Citations: 06)
8. Singh, G., Thomas, J., Wadhawa, S., Kashyap, A., Rahaman, S.A., Borkotoky, S., Datta, A., Singh, G.K., Mishra, I.B., Rai, G., Satija, J., Dubey, V.K., Modi, G. (2023). Repurposing the in‑house generated Alzheimer’s disease targeting molecules through computational and preliminary in‑vitro studies for the management of SARS‑coronavirus‑2. Molecular Diversity 28:2847–2862. https://doi.org/10.1007/s11030-023-10717-4 (IF:3.8; Citations: 04)
9. Sharma, M., Borkotoky, S., Dubey, V.K. (2023). Structure-based drug designing against Leishmania donovani using docking and molecular dynamics simulation studies: exploring glutathione synthetase as a drug target. Journal of Biomolecular Structure & Dynamics. 42(14):7628-7636. doi: https://doi.org/10.1080/07391102.2023.2240429 (IF:4.4; Citations: 08)
10. Ilyas, A., Poddar,N.K., Borkotoky, S*.(2023). Insights into the dynamic interactions of RNase A and osmolytes through computational approaches. Journal of Biomolecular Structure & Dynamics. 42(11):5903-5911. doi: https://doi.org/10.1080/07391102.2023.2229445 (IF:4.4; *corresponding author, Citations: 06)
11. Borkotoky, S*., Dey, D. (2023). Structural investigations of the palmitoylated F13 envelope protein of Mpox virus. Journal of Medical Virology, vol. 95, no. 5, p. e28798. doi: https://doi.org/10.1002/jmv.28798.
(IF: 4.6, *corresponding author, Citations: 02)
12. Borkotoky, S., Prakash, A., Modi, G.P., Dubey V.K. (2023). Computational Repurposing of Potential Dimerization Inhibitors against SARS-CoV-2 Main Protease. Letters in Drug Design & Discovery. vol.21, no.4, 799-808. (IF: 1.0, Citations: 01) http://dx.doi.org/10.2174/1570180820666230111141203
13. Joshi, A., Akhtar, N., Sharma, N.R., Kaushik, V., Borkotoky, S* (2023). MERS Virus Spike Protein HTL-Epitopes Selection and Multi-Epitope Vaccine Design Using Computational Biology. Journal of Biomolecular Structure & Dynamics. 41(22):12464-12479 https://doi.org/10.1080/07391102.2023.2191137 (IF: 4.4, Citations: 08; *corresponding author)
14. Borkotoky, S*., Dey, D., Hazarika (2022). Interactions of angiotensin-converting enzyme-2 (ACE2) and SARS-CoV-2 spike receptor-binding domain (RBD): A structural perspective. Molecular Biology Reports, 50, 2713–2721. https://doi.org/10.1007/s11033-022-08193-4. (IF: 2.8, Citations:74; *corresponding author)
15. Borkotoky, S*., Dey, D., Hazarika, Z., Joshi, A., & Tripathi, K. (2022). Unraveling viral dynamics through molecular dynamics simulations – A brief overview. Biophysical Chemistry, 291, 106908. https://doi.org/10.1016/j.bpc.2022.106908 (IF: 3.8, Citations: 17; *corresponding author)
BOOK CHAPTERS
16. Borkotoky, S*., Joshi, A., Kaushik, V., & Jha, A. N. (2022). Machine Learning and Artificial Intelligence in Therapeutics and Drug Development Life Cycle. In J. Akhtar, Badruddeen, M. Ahmad, & M. I. Khan (Eds.), Drug Development Life Cycle [Working Title]. IntechOpen. https://doi.org/10.5772/intechopen.104753 (Citations: 36; *corresponding author) ISBN: 978-1-80356-049-6
17. Rai, P.K., Joshi, A., Abraham, G., Saxena, R., Borkotoky, S., Yadav, R. K., Pandey, A. K., Tripathi, K. (2022). Cyanobacteria as a Source of Novel Bioactive Compounds. In Cyanobacteria as a Source of Novel Bioactive Compounds. https://doi.org/10.1002/9781119901198.ch6 Scrivener Publishing-Willey, 145-170. (Citations: 11) ISBN:9781119901198
18. Saxena, R., Joshi, A., Joshi, S, Borkotoky,S., Singh,K., Rai, P.K., Mueeda, Z. and Sharma, R.(2022). The role of artificial intelligence strategies to mitigate abiotic stress and climate change in crop production. In Visualization Techniques for Climate Change with Machine Learning and Artificial Intelligence. Elsevier, 273-292. https://doi.org/10.1016/B978-0-323-99714-0.00006-6 (Citations: 29) ISBN: 978-0-323-99714-0
19. Joshi, A., Borkotoky, S., Mehra, A., Kaushik,V.,Sahu,R., Farooq, A. (2023). Chapter 16 - Medical applications of functional antimicrobial nanoparticles, in Antiviral and Antimicrobial Coatings Based on Functionalized Nanomaterials, S. ul Islam, C. M. Hussain, and S. K. Shukla Eds.: Elsevier, 2023, pp. 515-541.doi: https://doi.org/10.1016/B978-0-323-91783-4.00015-2 (Citations: 03) ISBN: 978-0-323-91783-4
20. Borkotoky, S., Dey, D. (2023). Bioinformatics in Development of Antivirals. In: Mukhopadhyay, C.S., Choudhary, R.K., Panwar, H., Malik, Y.S. (eds) Biotechnological Interventions Augmenting Livestock Health and Production. Livestock Diseases and Management. Springer, Singapore. doi: https://doi.org/10.1007/978-981-99-2209-3_17 ISBN: 978-981-99-2209-3
21. Dey, D, Hazarika, Z., Pandey, A. K. and Borkotoky, S.* (2023) Chapter 07 - Livestock Viral Diseases and Insights into Systems Biology. Systems Biology, Bioinformatics and Livestock Science, Bentham, 19, pp 148-166. doi: https://doi.org/10.2174/9789815165616123010012 (Citations: 01) ISBN: 978-981-5165-61-6
22. Pandey AK, Borokotoky S, Tripathi K, Gautam A (2023). 13 - Interplay of hydrogen sulfide and plant metabolites under environmental stress. In: H₂S in Plants. Edited by Modolo LV, Da-Silva CJ, Singh VP, Tripathi DK, Fotopoulos V: Academic Press; 2024: 297-317. https://doi.org/10.1016/B978-0-323-99035-6.00004-X (Citations:08) ISBN: ISBN: 978-981-5165-61-6
PUBLICATIONS DURING THE POST-DOCTORAL PERIOD
23. Prakash A#, Borkotoky S#, Dubey VK (2022). Targeting two potential sites of SARS-CoV-2 Main Protease through computational drug repurposing. Journal of Biomolecular Structure & Dynamics. 41:7, 3014-3024. https://doi.org/10.1080/07391102.2022.2044907 (IF: 4.4, Citations: 11) (Equal First author)
24. Borkotoky S, Banerjee M, Modi GP, Dubey VK (2021). Identification of high affinity and low molecular alternatives of boceprevir against SARS-CoV-2 main protease: a virtual screening approach. Chemical Physics Letters. 770, 138446 https://doi.org/10.1016/j.cplett.2021.138446 (IF: 3.1, Citations: 21)
25. Borkotoky S, Dey D, Banerjee M (2021). Computational Insight into the Mechanism of SARS CoV-2 Membrane Fusion. Journal of Chemical Information and Modeling. 61(1):423-431. https://doi.org/10.1021/acs.jcim.0c01231 (IF: 5.3, Citations: 25)
26. Borkotoky S and Banerjee M (2020). A computational prediction of SARS-CoV-2 structural protein inhibitors from Azadirachta indica (Neem). Journal of Biomolecular Structure & Dynamics.39:11, 4111-4121. https://doi.org/10.1080/07391102.2020.1774419 (IF: 4.4, Citations: 170)
27. Dey D, Borkotoky S, Banerjee M (2020). In silico identification of Tretinoin as a SARS-CoV-2 envelope (E) protein ion channel inhibitor. Computers in Biology and Medicine, 127, 104063. https://doi.org/10.1016/j.compbiomed.2020.104063 (IF: 7.7, Citations: 71)
28. Nair P, Dey D, Borkotoky S, Shukla A, Banerjee M (2019). Hydrophobicity and oligomerization are essential parameters for membrane penetration activity of the VP4 peptide from the Hepatitis A Virus (HAV). Archives of Biochemistry and Biophysics,678, 108188 https://doi.org/10.1016/j.abb.2019.108188 (IF: 3.0 , Citations: 08)
PUBLICATIONS DURING Ph.D.
29. Borkotoky S, Murali A (2018). The highly efficient T7 RNA polymerase: A wonder macromolecule in biological realm. International Journal of Biological Macromolecules, 118, 49–56 https://doi.org/10.1016/j.ijbiomac.2018.05.198 (IF: 8.5, Citations: 106)
30. Borkotoky S, Meena CK, Bhalerao GM, and Murali A (2017). An in-silico glimpse into the pH dependent structural changes of T7 RNA polymerase: a protein with simplicity. Scientific Reports 7, 6290. https://doi.org/10.1038/s41598-017-06586-1 (IF: 3.9, Citations: 28)
31. Borkotoky S, Murali A (2017). A computational assessment of pH-dependent differential interaction of T7 lysozyme with T7 RNA polymerase. BMC Structural Biology 17(1):7. https://doi.org/10.1186/s12900-017-0077-9 (IF: 1.231, Citations: 45)
32. Borkotoky S, Meena CK and Murali A (2016). Interaction analysis of T7 RNA polymerase with heparin and its low molecular weight derivatives- an in silico approach. Bioinform Biol Insights,10,155–166. https://doi.org/10.4137/BBI.S40427 (IF: 2.4, Citations : 44)
33. Borkotoky S, Meena CK, Soman A, Murali A (2015). Insight into the LGP2 Helicase Domain – An in silico Approach. https://doi.org/10.13189/ijbb.2015.030202 International Journal of Biochemistry and Biophysics, 3, 13 - 23.
34. Borkotoky S, Meena CK, Khan MW, Murali A (2013). Three dimensional electron microscopy and in silico tools for macromolecular structure determination. EXCLI Journal;12,335-346. https://www.excli.de/index.php/excli/article/view/1152 (IF: 4.9, Citations: 07)
35. Borkotoky S*, Saravanan V, Jaiswal A, Das B, Selvaraj S, Murali A, and Lakshmi PTV (2013) The Arabidopsis stress responsive gene database, International journal of plant genomics, vol. 2013. 949564 https://doi.org/10.1155/2013/949564 (Scopus indexed, Citations: 60). (*corresponding author)
PUBLICATIONS IN COLLABORATION
36. Rajkumari J, Borkotoky S, Reddy D, Mohanty SK, Kumavath R, Murali A, Suchiang K, Busi S (2019). Anti-quorum sensing and anti-biofilm activity of 5-Hydroxymethylfurfural against Pseudomonas aeruginosa PAO1: insights from in vitro, in vivo and in silico studies. Microbiological Research, 226,19-26 https://doi.org/10.1016/j.micres.2019.05.001 (IF: 6.9, Citations : 74)
37. Alam P, Borkotoky S, Siddiqi Md K, Ehtram A, Majid N, Uddin M, and Khan RH (2018). DARK Classics in Chemical Neuroscience: Opium, a Friend or Foe. ACS Chemical Neuroscience, 10,182-189 https://doi.org/10.1021/acschemneuro.8b00546 (IF: 3.9, Citations :11)
38. Rajkumari J, Borkotoky S, Murali A, Busi S (2018). Anti-quorum sensing activity of Syzygium jambos (L.) Alston against Pseudomonas aeruginosa PAO1 and identification of its bioactive components. South African Journal of Botany, 118, 151-157 https://doi.org/10.1016/j.sajb.2018.07.004 (IF: 2.7, Citations: 29)
39. Rajkumari J, Borkotoky S, Murali A, Suchiang K, Mohanty SK, Busi S (2018). Cinnamic acid attenuates quorum sensing associated virulence factors and biofilm formation in Pseudomonas aeruginosa PAO1. Biotechnology Letters, 40: 1087-1100 https://doi.org/10.1007/s10529-018-2557-9 (IF: 2.5, Citations: 94)
40. Rajkumari J, Borkotoky S, Murali A, Suchiang K, Mohanty SK, Busi S (2018). Attenuation of quorum sensing controlled virulence factors and biofilm formation in Pseudomonas aeruginosa by pentacyclic triterpenes, betulin and betulinic acid. Microbial pathogenesis 118, 48-60. https://doi.org/10.1016/j.micpath.2018.03.012 (IF: 3.5, Citations: 114)
41. Meena CK, Borkotoky S, and Murali A (2016). Insight into virus encapsulation mechanism through in silico interaction study between coat protein and RNA operator loops of Sesbania mosaic virus. Molecular Omics (earlier known as Molecular Biosystems), 12, 1996-2009. https://doi.org/10.1039/C6MB00206D (IF: 2.4, Citations : 1)
42. Singh V, Borkotoky S, Murali A., Rao JL, Rao TG, & Dhoble SJ (2015). Electron paramagnetic resonance and photoluminescence investigation on ultraviolet-emitting gadolinium-ion-doped CaAl 12 O 19 phosphors. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 139, 1-6. https://doi.org/10.1016/j.saa.2014.11.097 (IF: 4.4, Citations : 43)