LIST OF PUBLICATIONS

2025

1. N. Mandal, S. L. Rath and D. Tripathy. Environmental Modulation of Coronavirus Structure and Function: Role of Temperature in Viral Pathogenesis. (Under Review)

2. P. Singh and S. L. Rath* Unraveling the Impact of Risk Factors on the Ferroptosis-Alzheimer’s Link for Early Detection.(Under Review)

3. 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)

4. Shwetlaxmi Patil, B Lakshmi, Sayan Manna, S. L. Rath, V Ravichandran Computational Approaches for Identifying Quorum Sensing Inhibitors (Under Review).

5. D. Tripathy, S. L. Rath, N. B. Debata and D. K. Chand. Synthesis, characterization and biological activity of binuclear palladium(II) complexes Results in Chemistry 15, I.F: 2.3, 102310, 2025

6. A Sarmah, N Shethia, P Rao, S. L. Rath, R Jobby, J B Aswathanarayan, V Ravichandran. MexB-Mediated Efflux Pumps in Pseudomonas aeruginosa: Mechanistic Insights, Inhibition Strategies, and Future Perspectives. ChemistrySelect 10 (17), e202500206.

2024

7. Arun D and S. L. Rath* Structural analysis of the impact of germline mutations of p16 in melanoma prone families Molecular Diversity I.F: 3.8, 2024, https://doi.org/10.1007/s11030-024-11089-z

8. A. Mahale and S. L. Rath*. Identification of Potential Therapeutic Compounds Targeting the VP1 Hydrophobic Pocket of Enterovirus-71 Capsid Protein Journal of Proteins and Proteomics I.F: 1.0, 2024, https://doi.org/10.1007/s42485-024-00169-1

9. A. Verma, R. Patel, A . Mahale, R. V. Thorat, S. L. Rath, E. Sridhar, A. Moiyadi and S. Srivastava*. Multiple Reaction Monitoring coupled with in silico drug repurposing identifies multitarget drug candidates against high-grade gliomas. OMICS: A Journal of Integrative Biology I.F: 3.978, 2024, https://doi.org/10.1089/omi.2023.0256

10. N. Mandal and S. L. Rath* Evaluating the Spike-hACE2 interactions in Wild-type and Variants of Concern of SARS-CoV-2 at different temperatures. Frontiers in Physics: Biophysics I.F. 3.718, 2024, 11, DOI: 10.3389/fphy.2023.1320437

2023

11. D. Banerjee*, S. L. Rath*, S. A. Darji and N. Mandal. Mutations in V84I A184V Of BLA TEM cluster plays a pivotal role n the dynamics of Ω-Loop leading to genesis of IR-TEM. J. Biomol. Struct. Dyn I. F. 5.235 2023, 1-13. DOI: 10.1080/07391102.2023.2291168

12. A. Joshi, S. Maurya, A. Mahale, S. L. Rath, T. Tripathi, A. K. Padhi. 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 I.F. 4.132 2023, 8, 41, 37852–37863

13. P. Venkatesham, S. R. Parcha, S. L. Rath, R. Chedupaka and R. R. Vedula. 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. I.F. 2.035 2023, 1. https://doi.org/10.1002/jhet.4728

14. P. Sahni, R. Gupta, D. Tripathy, S. L. Rath* and A. K. Pal* Ni(II)-polypyridyl complexes in DNA docking studies. New. J. Chem I. F. 3.25, 2023. https://doi.org/10.1039/D3NJ00961K

15. D. Tripathy, S. L. Rath, N. B. Debata, A. K. Pal, D. K. Chand and G. S. Hanan Platinum(II) Based Macrocyclic Host for Recognition of Aromatic Hydrocarbons. J. Mol. Struct ,1292, 136104, 2023 (I.F 3.841) 10.1016/j.molstruc.2023.136104 

16. S. Mohanty#, S. L. Rath#, P. Sharma, Y. Ahmad*. 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 Genetics, 7, 3, 2023. doi:10.21926/obm.genet.2303186

17. N. Mandal and S. L. Rath* Identification of inhibitors against SARS-CoV-2 Variants of Concern using Virtual Screening and Metadynamics-based enhanced sampling. Chem. Phys, 111995, 2023 (I.F 2.552)

2022

18. D. Bisht, S. L. Rath* , S. Roy and A. Jaiswal*. MoS2 nanosheets effectively binds and destabilizes the SARS-CoV-2 Spike spike protein and human ACE2 receptor interactions. Soft Matter,18, 8961-8973 (2022) (I.F. 4.01)

19. S. L. Rath*, M. Tripathy* and N. Mandal How does temperature affect the dynamics of SARS-CoV-2 M proteins? Insights from Molecular Dynamics Simulations, J. Mem. Biol., 255, pages 341–356 (2022) (I.F: 1.84)

20. N. Mandal, A. K. Padhi and S. L. Rath* Molecular Insights into the Differential Dynamics of SARS-CoV-2 Variants of Concern (VOC) J. Mol. Graph. Model, 114, 108194, 2022 (I.F: 2.518)

21. D. Tripathy, S. Ghanta, S. L. Rath and D. K. Chand. Hierarchical self-assembly of self-assembled Pd(II) complexes: synthesis, structural characterization, crystal packing evaluation and docking studies. J. Mol. Struct, 1259, 132767, 2022 (I.F: 3.841)

22. S. L. Rath*, A. K. Padhi and N. Mandal. Scanning the RBD-ACE2 Molecular Interactions in Omicron Variant. Biochem. Biophys. Res. Commun. 592,18-23, 2022 (I.F: 3.575)

2021

23. A. K. Padhi, S. L. Rath and T. Tripathi* Accelerating COVID-19 Research Using Molecular Dynamics Simulation. J. Phys. Chem B. 125, 9078-9091, 2021 [Cover image] (I.F: 2.991) 

24. N. Sarkar, A. Thakur, J. Ghadge, S.L. Rath* Computational studies reveal Fluorine based quinolines to be potent inhibitors for proteins involved in SARS-CoV-2 assembly.  J. Fluor. Chem. 250, 109865, 2021 (I.F: 2.05)

25. D. Tripathy*, A. K. Pal, S. L. Rath, G. S. Hanan, B. B. Panda, D. K. Chand. Synthesis, characterization and molecular docking study of Nitro-4'-(2-pyridyl)-2,2':6',2''-terpyridyl palladium(II) nitrate. Inorg. Chem. Commun. 126, 108494, 2021 (I.F: 2.495)

26. H. G. Toor, D.I. Banerjee*, S. L. Rath, S. A. Darji. Computational drug re-purposing targeting the Spike glycoprotein of SARS-CoV-2 as an effective strategy to neutralize COVID-19.  Eur. J. Pharmacol. 890, 173720, 2021 (I.F :3.170)

2020

27. S. L. Rath*, Kishant Kumar. Investigation of the effect of temperature on the structure of SARS-Cov-2 Spike Protein by Molecular Dynamics Simulations. Front Mol Biosci 7, 297, Sept 22, 2020 : DOI: 10.3389/fmolb.2020.583523  (I. F : 4.62)

Before 2020

28. S. L. Rath, H.Liu, S. Okazaki, W. Shinoda*. Identification of Factors Promoting HBV Capsid Self-Assembly by Assembly-Promoting Antivirals. J. Chem Inf Model 58,328, Feb 26, 2018 DOI: 10.1021/acs.jcim.7b00471. (I.F: 5.246)

29. S. L. Rath, S. Senapati*. Mechanism of p27 Unfolding for CDK2 Reactivation Scientific Reports 6, 26450, 2016 DOI:10.1038/srep26450 (I.F: 3.998)

30. S. L. Rath, S. Senapati*. Why are the truncated Cyclin E1s more effective CDK2 activators than the full-length isoforms? Biochemistry June 20, 2014 DOI: 10.1021/bi5004052. (I.F: 2.952)

31. S. L. Rath, S. Senapati*. Molecular basis of differential selectivity of cyclobutyl-substituted imidazole inhibitors against CDKs: Insights for rational drug design. PLOS One 8(9):1-10, 2013. (I.F: 3.240)

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 (Proofread)

CONFERENCES 

Conference Presentations

Oral

1. 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

2. 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

3. 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

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

5. 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.

6. 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 2 nd to December 4 th 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)
    

Before 2020

15. 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”.

16. 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”.

17. ​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)

18. 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)

19. 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

20. 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”.

21. 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]