LIST OF PUBLICATIONS

2026

1. P. Paharwar and S. L. Rath* Markerless Augmented Reality Based Framework for Post-Operative Lower-Limb Rehabilitation Using Real-Time Pose Estimation (Under Review)

2. P. Singh and S. L. Rath* Neural Network-Enhanced Investigation of Ferroptosis and Druggability in Early-Onset Alzheimer’s Disease. (https://www.biorxiv.org/cgi/content/short/2025.06.21.660896v1) (Under Review)

3. Lin Zhong, Shwetlaxmi Patil, Lakshmi B, Pratibha Singh, S. L. Rath and Vinothkannan Ravichandran. Computational Approaches for Identifying Quorum Sensing Inhibitors (Under Review).

4. Tella, P.; Rath, S. L.* Site-specific phosphorylation modulates p16/CDK4 binding dynamics and energetics: Insights from molecular simulations. Biochem. Biophys. Res. Commun. Accepted. Impact Factor: 2.2.

5. Singh, P.; Rath, S. L.* Unraveling the impact of risk factors on the ferroptosis-Alzheimer’s link for early detection. J. Alzheimers Dis. J Alzheimers Dis. 2026, 109(4):1834-1857. Impact Factor: 3.1.

2025

6. Tripathy, D.; Rath, S. L.; Debata, N. B.; Chand, D. K. Synthesis, characterization and biological activity of binuclear palladium(II) complexes. Results Chem. 2025, 15, 102310. Impact Factor: 4.2.

7. Sarmah, A.; Shethia, N.; Rao, P.; Rath, S. L.; Jobby, R.; Aswathanarayan, J. B.; Ravichandran, V. MexB-mediated efflux pumps in Pseudomonas aeruginosa: Mechanistic insights, inhibition strategies, and future perspectives. ChemistrySelect 2025, 10(17), e202500206. Impact Factor: 2.0.

8. Arun, D.; Rath, S. L.* Structural analysis of the impact of germline mutations of p16 in melanoma-prone families. Mol. Divers. 2025, 1–11. https://doi.org/10.1007/s11030-024-11089-z. Impact Factor: 3.8.

2024

9. Mahale, A.; Rath, S. L.* Identification of potential therapeutic compounds targeting the VP1 hydrophobic pocket of Enterovirus-71 capsid protein. J. Proteins Proteom. 2024, 1–11. Impact Factor: 1.0.

10. Verma, A.; Patel, R.; Mahale, A.; Thorat, R. V.; Rath, S. L.; Sridhar, E.; Moiyadi, A.; Srivastava, S.* Multiple reaction monitoring coupled with in silico drug repurposing identifies multitarget drug candidates against high-grade gliomas. OMICS 2024. https://doi.org/10.1089/omi.2023.0256. Impact Factor: 1.6.

11. Mandal, N.; Rath, S. L.* Evaluating the Spike-hACE2 interactions in wild-type and variants of concern of SARS-CoV-2 at different temperatures. Front. Phys. 2023, 11. DOI: 10.3389/fphy.2023.1320437. Impact Factor: 4.6.

2023

12. Banerjee, D.; Rath, S. L.; Darji, S. A.; Mandal, N. Mutations V84I and A184V of BLA TEM cluster play a pivotal role in the dynamics of Ω-loop leading to genesis of IR-TEM. J. Biomol. Struct. Dyn. 2023, 1–13. DOI: 10.1080/07391102.2023.2291168. Impact Factor: 2.7.

13. Joshi, A.; Maurya, S.; Mahale, A.; Rath, S. L.; Tripathi, T.; Padhi, A. K. Delineating the structure-dynamics-binding differences among BA.1, BA.4/5, and BF.7 SARS-CoV-2 variants through atomistic simulations: Correlation with structural and epidemiological features. ACS Omega 2023, 8(41), 37852–37863. Impact Factor: 4.3.

14. Venkatesham, P.; Parcha, S. R.; Rath, S. L.; Chedupaka, R.; Vedula, R. R. New one-pot synthesis of imidazo[2,1-b][1,2,4]triazoles, 1,2,4-triazolo iminoindoline-2-ones and in vitro antibacterial activity, B-DNA study. J. Heterocycl. Chem. 2023. https://doi.org/10.1002/jhet.4728. Impact Factor: 2.4.

15. Sahni, P.; Gupta, R.; Tripathy, D.; Rath, S. L.; Pal, A. K. Ni(II)-polypyridyl complexes in DNA docking studies. New J. Chem. 2023. https://doi.org/10.1039/D3NJ00961K. Impact Factor: 2.5.

16. Tripathy, D.; Rath, S. L.; Debata, N. B.; Pal, A. K.; Chand, D. K.; Hanan, G. S. Platinum(II)-based macrocyclic host for recognition of aromatic hydrocarbons. J. Mol. Struct. 2023, 1292, 136104. https://doi.org/10.1016/j.molstruc.2023.136104. Impact Factor: 4.7.

17. Mohanty, S.#; Rath, S. L.#; Sharma, P.; Ahmad, Y.* An evidence of drug repurposing for COVID-19 pandemic based on in silico investigation from phenolic derivatives of Silybum marianum against SARS-CoV-2 proteins. OBM Genet. 2023, 7(3). DOI: 10.21926/obm.genet.2303186.

18. Mandal, N.; Rath, S. L.* Identification of inhibitors against SARS-CoV-2 variants of concern using virtual screening and metadynamics-based enhanced sampling. Chem. Phys. 2023, 111995. Impact Factor: 2.4.

2022

19. Bisht, D.; Rath, S. L.; Roy, S.; Jaiswal, A. MoS2 nanosheets effectively bind and destabilize the SARS-CoV-2 spike protein and human ACE2 receptor interactions. Soft Matter 2022, 18, 8961–8973. Impact Factor: 2.8.

20. Rath, S. L.; Tripathy, M.; Mandal, N. How does temperature affect the dynamics of SARS-CoV-2 M proteins? Insights from molecular dynamics simulations. J. Membr. Biol. 2022, 255, 341–356. Impact Factor: 2.9.

21. Mandal, N.; Padhi, A. K.; Rath, S. L.* Molecular insights into the differential dynamics of SARS-CoV-2 variants of concern (VOC). J. Mol. Graph. Model. 2022, 114, 108194. Impact Factor: 3.0.

22. Tripathy, D.; Ghanta, S.; Rath, S. L.; Chand, D. K. Hierarchical self-assembly of self-assembled Pd(II) complexes: Synthesis, structural characterization, crystal packing evaluation and docking studies. J. Mol. Struct. 2022, 1259, 132767. Impact Factor: 4.7.

23. Rath, S. L.*; Padhi, A. K.; Mandal, N. Scanning the RBD-ACE2 molecular interactions in Omicron variant. Biochem. Biophys. Res. Commun. 2022, 592, 18–23. Impact Factor: 2.2.

2021

24. Padhi, A. K.; Rath, S. L.; Tripathi, T.* Accelerating COVID-19 research using molecular dynamics simulation. J. Phys. Chem. B 2021, 125, 9078–9091. Cover Image. Impact Factor: 3.46.

25. Sarkar, N.; Thakur, A.; Ghadge, J.; Rath, S. L.* Computational studies reveal fluorine-based quinolines to be potent inhibitors for proteins involved in SARS-CoV-2 assembly. J. Fluor. Chem. 2021, 250, 109865. Impact Factor: 1.9.

26. Tripathy, D.*; Pal, A. K.; Rath, S. L.; Hanan, G. S.; Panda, B. B.; Chand, D. K. Synthesis, characterization and molecular docking study of Nitro-4'-(2-pyridyl)-2,2':6',2''-terpyridyl palladium(II) nitrate. Inorg. Chem. Commun. 2021, 126, 108494. Impact Factor: 5.4.

27. Toor, H. G.; Banerjee, D. I.*; Rath, S. L.; Darji, S. A. Computational drug re-purposing targeting the spike glycoprotein of SARS-CoV-2 as an effective strategy to neutralize COVID-19. Eur. J. Pharmacol. 2021, 890, 173720. Impact Factor: 4.7.

2020

28. Rath, S. L.*; Kumar, K. Investigation of the effect of temperature on the structure of SARS-CoV-2 spike protein by molecular dynamics simulations. Front. Mol. Biosci. 2020, 7, 297. DOI: 10.3389/fmolb.2020.583523. Impact Factor: 4.0.

Before 2020

29. Rath, S. L.; Liu, H.; Okazaki, S.; Shinoda, W.* Identification of factors promoting HBV capsid self-assembly by assembly-promoting antivirals. J. Chem. Inf. Model. 2018, 58, 328. DOI: 10.1021/acs.jcim.7b00471. Impact Factor: 5.3.

30. Rath, S. L.; Senapati, S.* Mechanism of p27 unfolding for CDK2 reactivation. Sci. Rep. 2016, 6, 26450. DOI: 10.1038/srep26450. Impact Factor: 3.9.

31. Rath, S. L.; Senapati, S.* Why are the truncated Cyclin E1s more effective CDK2 activators than the full-length isoforms? Biochemistry 2014. DOI: 10.1021/bi5004052. Impact Factor: 3.0.

32. Rath, S. L.; Senapati, S.* Molecular basis of differential selectivity of cyclobutyl-substituted imidazole inhibitors against CDKs: Insights for rational drug design. PLoS One 2013, 8(9), 1–10. Impact Factor: 2.6.

BOOK CHAPTERS

1. S. Kaushik, S. L. Rath, S. C. Kundu and R. L. Reis. Protein Structure Visualization. Reference Module in Life Sciences. Elsevier Inc. June 2018. DOI: 10.1016/B978-0-12-809633-8.20283-5.

2. S. L. Rath, S. Mohanty and D. Tripathy. Biofertilizers: A representative illustration of plant-microbe interaction. New India Publishing Agency, New Delhi. ISBN: 9789390175031 

3. MANDAL, N. and RATH, S.L., 2024. Target-Based Drug Designing. Computational Biology in Drug Discovery and Repurposing, p.109. ISBN: 978-1-77491-556-1

4. Rath, S.L. and Tripathy, D., 2024. Design and development of vaccines through computational approaches. In Bioreactor Design Concepts for Viral Vaccine Production (pp. 417-427). Academic Press. ISBN: 978-0-443-15378-5

5. N. Mandal, D. Arun and S. L. Rath, 2025. In silico methods to study biofilms. Methods for the Study of Microbial Biofilms: Current Trends and Recent Advancements 2026, Pages 17-30

CONFERENCES 

Conference Presentations

Oral

1. Pratibha Singh and S. L. Rath on the topic “Decoding ferroptosis in Alzheimer’s disease: a multi-risk factor and biomarker-based analysis” at the  CETSB26 conference  organized by the National Institute of Technology Warangal (Best Oral Presentation)

2. Arun D and S. L. Rath, HSCB-2025, IIt Hyderabad. Title: "Structural analysis of the impact of germline mutations of p16 in melanoma prone families". Feb 28-Mar 1, 2025

3. S. L. Rath, N. Mandal and M. Tripathy, Compflu 2021. Title: “How does temperature affect the dynamics of SARS-CoV-2 M proteins? Insights from Molecular Dynamics Simulations”, Dec 13-15, 2021

4. S. L. Rath, N. Mandal and M. Tripathy, Physical Chemistry Physical Biology Conference India. Title: “How does temperature affect the dynamics of SARS-CoV-2 M proteins? Insights from Molecular Dynamics Simulations”, 24-28 Sept, 2021

5. S. L. Rath, Covid-19 Drug and Diagnostics Development. Title :“Temperature and its effect on the SARS-CoV-2 structural proteins” , Feb 6, 2021

6. N. Mandal and S. L. Rath* Computer Simulation and Theory of Macromolecules 2022 organized by Max Planck Institute for Multidisciplinary Science in Hünfeld, Germany Title: “Mechanistic Insights into the Differential Dynamics of SARS-CoV-2 Variants of Concern (VOC)" 8-9th April, 2022.

7. N. Mandal and S. L. Rath* 5th International Conference on Advances in Biosciences and Biotechnology ICABB-2022, organized by Department of Biotechnology, Jaypee Institute of Information Technology. Title “Evaluation of binding of small molecule inhibitors against SARS-CoV-2 Variants of Concern” 20th-22nd January, 2022.

Poster Presentation

1. Nabanita Mandal and Soumya Lipsa Rath* on the topic “Evaluating the Spike-hACE2 interactions in Wild-type and Variants of Concern of SARS-CoV-2 at different temperatures” at the International Conference on Recent Advances in Biotechnology (icRAB -2022) organized by Dr B R Ambedkar National Institute of Technology Jalandhar from December 2nd to December 4th 2022.

2. Nabanita Mandal and Soumya Lipsa Rath* on the topic “Identification of inhibitors against SARS-CoV-2 Variants of Concern using Virtual Screening and Metadynamics-based enhanced sampling” at the Biological Engineering Society Conference (BESCON -2022), organized by IIT Kharagpur and Bose Institute, Kolkata from November 4 th to November 6 th 2022.

3. Nabanita Mandal and Soumya Lipsa Rath* on the topic “Unravelling the binding affinity of SARS-CoV-2 VOCs using MD Simulations” at National Conference on Molecular Modelling and simulations, 2022, organized by VIT, Bhopal.

4. Nabanita Mandal and Soumya Lipsa Rath* on the topic “Evaluating the impact of temperature on SARS-CoV-2 Spike/ACE2complex in Wild-Type and Variants of Concern” at Soft Matter Day at IIT Hyderabad on 13th May, 2023.

5. Nabanita Mandal and Soumya Lipsa Rath* on the topic “Virtual Screening and Metadynamics to identify inhibitors against SARS-CoV-2 Variants of Concern ” at Department of Chemistry, NIT Warangal at the International Conference on Organic and Medicinal Chemistry Conference held from June 28th-30th, 2023.

6. Soumya Lipsa Rath, V. Gayatri Tamma and Smaranika Mohaptra on the topic "Identifying antibiotic resistant mutants in β-lactamases for Class A and Class B using unsupervised Machine Learning" at the 2-days International Conference on Recent Advances on Science and Engineering (RAiSE 2023) organized by MAHE, Dubai from 4th-5th October, 2023.

7. Nabanita Mandal and Soumya Lipsa Rath on the topic “Evaluating the impact of temperature on SARS- CoV-2 Spike/ACE2complex in Wild-Type and Variants of Concern” at MD@60, organized by JNCASR and CECAM from February 25th to February 29th, 2024.

8. Nabanita Mandal and Soumya Lipsa Rath presented a poster on the topic “Evaluating the impact of temperature on SARS- CoV-2 Spike/ACE2complex in Wild-Type and Variants of Concern” at the Society of Biological Chemists, organized by BITS-Goa from December 18th to December 20th, 2023.

9. Pratibha Singh and Soumya Lipsa Rath on the topic “Machine learning and Neural- network based investigation of the link between Ferroptosis and early onset of Alzheimer’s Disease” at the International Symposium on Physics of Cells and Tissues 2.0 (PoCT 2.0 2024) organized by Indian Institute of Science Bangalore from 21st to 22nd June, 2024.

10. Pavan Kumar RS and Soumya Lipsa Rath on the topic "Exploring Transition Metal Complexes as Potential Inhibitors for G-Quadruplex Structures" at “HySci 2024” conference organized by Indian institute of Technology Hyderabad on April 20th, 2024.

11. Arun D and Soumya Lipsa Rath on the topic "Structural analysis of the impact of germline mutations of p16 in melanoma prone families" at “HySci 2024” conference organized by Indian institute of Technology Hyderabad on April 20th, 2024.

12. Pratibha Singh and Soumya Lipsa Rath on the topic “Machine learning and Neural- network based investigation of the link between Ferroptosis and early onset of Alzheimer’s Disease” at the international conference IMMUNOCON 2024 organized by the Department of Biochemistry, Indian Institute of Sciences, Bangalore from October 14th, 2024 to October 20th, 2024.

13. Pratibha Singh and Soumya Lipsa Rath on the topic “Machine learning and Neural- network based investigation of the link between Ferroptosis and early onset of Alzheimer’s Disease” at the  HSCB 2025 conference  jointly organized by the Indian Institute of Technology Hyderabad (IITH) and the University of Hyderabad (UoH)

14. Lakshmi B and Soumya Lipsa Rath on the topic “Identification of Potential Efflux pump Inhibitors against MexB through Virtual Screening and Computer-based Simulations” at the  HSCB 2025 conference  jointly organized by the Indian Institute of Technology Hyderabad (IITH) and the University of Hyderabad (UoH)

15. Pratibha Singh and S. L. Rath on the topic "DECODING FERROPTOSIS IN ALZHEIMER’S DISEASE: A MULTI- RISK FACTOR AND BIOMARKER-BASED ANALYSIS" in Genomics India Conference 2025, held from August 12–14, 2025, at the J N Tata Auditorium, IISc, Bengaluru.

16. Pratibha Singh and S. L. Rath on the topic "DECODING FERROPTOSIS IN ALZHEIMER’S DISEASE: A MULTI- RISK FACTOR AND BIOMARKER-BASED ANALYSIS" at AD/PDTM26: 20th International Conference on Alzheimer’s & Parkinson’s Diseases taking place Online and in Copenhagen, Denmark from 17-21 March, 2026.

17. Pratibha Singh and S. L. Rath on the topic "DECODING FERROPTOSIS IN ALZHEIMER’S DISEASE: A MULTI- RISK FACTOR AND BIOMARKER-BASED ANALYSIS" Research Scholar's Confluence held from 19th- 20th September, 2025 at NITW. (Best Poster)

18. Anirudh R and S. L. Rath Analysis and in silico discovery of driver genes and pathways facilitated by Mapk4 in cancer progression: a graphical approach at the  CETSB26 conference organized by the National Institute of Technology Warangal

19. Anoushka Chatterjee, Vahini Yanduri, Akshaya Vasudevan, Pratibha Singh* and S. L. Rath* PartnerIDP: Predicting Interaction-Driven Conformations of IDPs Using Machine Learning at the  CETSB26 conference  organized by the National Institute of Technology Warangal.

20. Prachi Paharwar and S. L. Rath on the to “Immersive structural biophysics: AR/VR-based interactive visualization of protein structure, dynamics, and function” at the  CETSB26 conference  organized by the National Institute of Technology Warangal. 

21. Pavani Tella and S. L. Rath on the topic “Phosphorylation associated binding effects of p16 towards CDK4” at the  CETSB26 conference  organized by the National Institute of Technology Warangal. 

22. Pratibha Singh and S. L. Rath on the topic “Decoding ferroptosis in Alzheimer’s disease: a multi-risk factor and biomarker-based analysis” at the  CETSB26 conference  organized by the National Institute of Technology Warangal.

Before 2020

23. S. L. Rath, S. Senapati., Theoretical Chemistry Symposium (TCS), 2010 at IIT Kanpur, Kanpur, India. Title: “A structure-function co-relation study of CDK2-Cyclin E complexes”.

24. S. L. Rath, S. Senapati., Medchem, 2011 at IIT Madras, Chennai, India. Title: “Molecular dynamics simulations of 4-aminoimidazole based inhibitor bound activated CDK2 and CDK5 complexes”.

25. ​S. L. Rath, S. Senapati., Biomers, 2012 at Department of Biotechnology, IIT Madras. Title: “Understanding the structure and dynamics of Cyclin Dependent Kinases using Molecular Dynamics Simulation”. (Oral Presentation)

26. S. L. Rath, S. Senapati., International Conference on Biomolecular Simulations and Dynamics, November 2013, IIT Madras, Title: “Why are the truncated Cyclin E1s more effective CDK2 activators than the full- length isoforms?” (Oral Presentation)

27. S. L. Rath, S. Senapati., 27th Annual Symposium of Protein Society, July 22nd 2013, Boston, Massachusetts, USA. Title: “The Structural Basis of Higher Activity of Truncated Cyclin E1-CDK2 Complexes in Tumor Cells”. DOI: 10.1002/pro.2303

28. S. L. Rath, S. Senapati., MD@50, a conference held to commemorate the fiftieth year of the publication of seminal paper of Dr. Aneesur Rahman, Aug 27th 2014, Jawaharlal Nehru Centre for Advanced Science and Research, Bengaluru, Karnataka, India. Title: “The Mechanism of re-activation of CDK2 upon phosphorylation of its inhibitor, p27”.

29. S. L. Rath, S. Senapati., Shaastra Research Expo, Jan 2nd 2015, IIT Madras, Chennai, India. Title: “The Mechanism of re-activation of CDK2 upon phosphorylation of its inhibitor, p27”.

PATENTS

1. P. Singh and Rath S.L., A Diagnostic Method For Early Detection Of Alzheimer’s Disease Via Ferroptosis-Related Gene Signatures And Risk Factor Integration. Patent Application No. 202541088716.

CONFERENCE PROCEEDINGS

2. Rath S.L., Sinha C., Kasturi S.L.N.P., Mohapatra S., Jain K. (2022) An Unsupervised Clustering Algorithm to Cluster the New SARS-CoV-2 Virus Mutation. In: Saini H.S., Sayal R., Govardhan A., Buyya R. (eds) Innovations in Computer Science and Engineering. Lecture Notes in Networks and Systems, vol 385. Springer, Singapore. https://doi.org/10.1007/978-981-16-8987-1_19 [Best conference Paper]

3. Tripathy, D., Rath, S.L., Mishra, S.S., Chand, D.K. (2023). Nanoscopic Pd(II)-Based Complexes with Poly-Ether Functionalized Ligand: The Crown Ether Analog. In: Rao, N.M., Lingamallu, G., Agarwal, M. (eds) Advanced Nanomaterials and Their Applications. ICANA 2022. Springer Proceedings in Materials, vol 22. Springer, Singapore. https://doi.org/10.1007/978-981-99-1616-0_4

4. Rath S.L., Mohapatra S., and Veena Gayathri. Identifying antibiotic resistant mutants in β-lactamases for Class A and Class B using unsupervised Machine Learning Eng. Proc. 2023, 59(1), 146; https://doi.org/10.3390/engproc2023059146 [Best conference Paper]