Peer-Reviewed Publications
2024
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Kashyap, D., Koirala, S.,
Roy, R.,
Saini, V., Varshney, N., Bagde, P.H., Samanta, S., Kar, P., and Jha, H.C., 2024.
Computational insights into VacA toxin inhibition: harnessing FDA-approved antibiotics against Helicobacter pylori.
Journal of Biomolecular Structure and Dynamics, 42(24), pp.13725–13737.
DOI -
Poddar, S.,
Roy, R.,
and Kar, P., 2024.
Elucidating the conformational dynamics of histo-blood group antigens and their interactions with the rotavirus spike protein through computational lens
Journal of Biomolecular Structure and Dynamics, 42(23), pp.13201-13215.
DOI -
Kashyap, D.,
Roy, R.,
Varshney, N., Baral, B., Bagde, P.H., Kandpal, M., Kumar, S., Kar, P. and Jha, H.C., 2024.
Withania somnifera extract reduces gastric cancerous properties through inhibition of gankyrin in cellular milieu produced by Helicobacter pylori and Epstein Barr virus
Journal of Biomolecular Structure and Dynamics, 42(18), pp.9399-9415.
DOI -
Koirala, S.#,
Roy, R.#,
Samanta, S., Mahapatra, S. and Kar, P., 2024.
Plant derived active compounds of ayurvedic neurological formulation, Saraswatharishta as a potential dual leucine zipper kinase inhibitor: An in-silico study.
Journal of Biomolecular Structure and Dynamics, 42(20), pp.11201-11214.
DOI -
Mukherjee, A., Paul, A.,
Roy, R.,
and Ghosh, K., 2024
The role of extrinsic and intrinsic factors in perceptual filling-in of the blind-spot with variegated color and texture stimuli.
Vision Research, 222, p.108452.
DOI -
Are, V.N.,
Roy, R.,
Dhanda, S.K., Neema, S., Sahu, N.R., Adithya, N., Tiwari, R., Kar, P. and Nayak, D., 2024.
Predicting immune response targets in orthoflaviviruses through sequence homology and computational analysis.
Journal of Molecular Modeling, 30(8), p.295.
DOI -
Singh, S., Ghosh, P.,
Roy, R.,
Behera, A., Sahadevan, R., Kar, P., Sadhukhan, S. and Sonawane, A., 2024.
4 ″-Alkyl EGCG Derivatives Induce Cytoprotective Autophagy Response by Inhibiting EGFR in Glioblastoma Cells.
ACS omega, pp.2286-2301.
DOI -
Poddar, S.,
Roy, R.,
and Kar, P., 2024.
The conformational dynamics of Hepatitis C Virus E2 glycoprotein with the increasing number of N-glycosylation unraveled by molecular dynamics simulations.
ACS omega, pp.2286-2301.
DOI
2023
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Jaiswal, A.,
Roy, R.,
Tamrakar, A., Singh, A.K., Kar, P. and Kodgire, P., 2023.
Activation-induced cytidine deaminase an antibody diversification enzyme interacts with chromatin modifier UBN1 in B-cells..
Scientific Reports, 13(1), p.19615.
DOI -
Roy, R.,
Sk, M.F., Tanwar, O. and Kar, P., 2023.
Computational studies indicated the effectiveness of human metabolites against SARS-Cov-2 main protease..
Molecular Diversity, 27(4), pp.1587-1602.
DOI -
Kashyap, D.#,
Roy, R.#,
Kar, P. and Jha, H.C., 2023.
Plant-derived active compounds as a potential nucleocapsid protein inhibitor of SARS-CoV-2: an in-silico study..
Journal of Biomolecular Structure and Dynamics, 41(10), pp.4770-4785.
DOI -
Roy, R.,
Poddar, S., Sk, M.F. and Kar, P., 2023.
Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: Insights from 20 μs long atomistic molecular dynamic simulations..
Journal of Biomolecular Structure and Dynamics, 41(8), pp.3305-3320.
DOI
2022
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Roy, R.,
Poddar, S. and Kar, P., 2022.
Comparison of the conformational dynamics of an N-glycan in implicit and explicit solvents..
Carbohydrate Research, 522, p.108700.
DOI -
Roy, R.,
Sk, M.F., Jonniya, N.A., Poddar, S. and Kar, P., 2022.
Finding potent inhibitors against SARS-CoV-2 main protease through virtual screening, ADMET, and molecular dynamics simulation studies..
Journal of Biomolecular Structure and Dynamics, 40(14), pp.6556-6568.
DOI -
Rehman, S., Bishnoi, S.,
Roy, R.,
Kumari, A., Jayakumar, H., Gupta, S., Kar, P., Pattnaik, A.K. and Nayak, D., 2022.
Emerging biomedical applications of the vesicular stomatitis virus glycoprotein..
ACS omega, 7(37), pp.32840-32848.
DOI -
Jaiswal, S.,
Roy, R.,
Dutta, S.B., Bishnoi, S., Kar, P., Joshi, A., Nayak, D. and Gupta, S., 2022.
Role of doxorubicin on the loading efficiency of ICG within silk fibroin nanoparticles..
ACS Biomaterials Science & Engineering, 8(7), pp.3054-3065.
DOI -
Roy, R.,
Jonniya, N.A. and Kar, P., 2022.
Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study..
The Journal of Physical Chemistry B, 126(21), pp.3852-3866.
DOI -
Roy, R.,
Jonniya, N.A., Sk, M.F. and Kar, P., 2022.
Comparative structural dynamics of isoforms of helicobacter pylori adhesin BabA bound to Lewis b hexasaccharide via multiple replica molecular dynamics simulations..
Frontiers in Molecular Biosciences, 9, p.852895.
DOI -
Sk, M.F., Jonniya, N.A.,
Roy, R.,
and Kar, P., 2022.
Phosphorylation-induced conformational dynamics and inhibition of Janus Kinase 1 by suppressors of cytokine signaling 1..
The Journal of Physical Chemistry B, 126(17), pp.3224-3239.
DOI -
Roy, R.#,
Mishra, A.#, Poddar, S., Nayak, D. and Kar, P., 2022
Investigating the mechanism of recognition and structural dynamics of nucleoprotein-RNA complex from Peste des petits ruminants virus via Gaussian accelerated molecular dynamics simulations..
Journal of Biomolecular Structure and Dynamics, 40(5), pp.2302-2315.
DOI -
Sk, M.F., Jonniya, N.A.,
Roy, R.,
and Kar, P., 2022.
Unraveling the molecular mechanism of recognition of selected next-generation antirheumatoid arthritis inhibitors by Janus kinase 1..
ACS omega, 7(7), pp.6195-6209.
DOI -
Jonniya, N.A., Sk, M.F.,
Roy, R.,
and Kar, P., 2022.
Discovery of potential competitive inhibitors against With-No-Lysine kinase 1 for treating hypertension by virtual screening, inverse pharmacophore-based lead optimization, and molecular dynamics simulations..
SAR and QSAR in Environmental Research, 33(2), pp.63-87.
DOI -
Singh, S., Sahadevan, R.,
Roy, R.,
Biswas, M., Ghosh, P., Kar, P., Sonawane, A. and Sadhukhan, S., 2022.
Structure-based design and synthesis of a novel long-chain 4′′-alkyl ether derivative of EGCG as potent EGFR inhibitor: In vitro and in silico studies..
RSC advances, 12(28), pp.17821-17836.
DOI
2021
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Roy, R.,
Jonniya, N.A., Poddar, S., Sk, M.F. and Kar, P., 2021
Unraveling the molecular mechanism of recognition of human interferon-stimulated gene product 15 by coronavirus papain-like proteases: A multiscale simulation study.
Journal of Chemical Information and Modeling, 61(12), pp.6038-6052.
DOI -
Sk, M.F., Haridev, S.,
Roy, R.,
and Kar, P., 2021.
Investigating potency of TMC-126 against wild-type and mutant variants of HIV-1 protease: a molecular dynamics and free energy study.
SAR and QSAR in Environmental Research, 32(11), pp.941-962
DOI -
Sk, M.F.,
Roy, R.,
Jonniya, N.A., Poddar, S. and Kar, P., 2021.
Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations.
Journal of Biomolecular Structure and Dynamics, 39(10), pp.3649-3661.
DOI -
Sk, M.F.,
Roy, R.,
and Kar, P., 2021.
Exploring the potency of currently used drugs against HIV-1 protease of subtype D variant by using multiscale simulations.
Journal of Biomolecular Structure and Dynamics, 39(3), 988-1003.
DOI -
Thurakkal, L., Singh, S.,
Roy, R.,
Kar, P., Sadhukhan, S. and Porel, M., 2021.
An in-silico study on selected organosulfur compounds as potential drugs for SARS-CoV-2 infection via binding multiple drug targets.
Chemical physics letters, 763, p.138193.
DOI
2020
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Sk, M.F., Jonniya, N.A.,
Roy, R.,
Poddar, S. and Kar, P., 2020.
Computational investigation of structural dynamics of SARS-CoV-2 methyltransferase-stimulatory factor heterodimer nsp16/nsp10 bound to the cofactor SAM.
Frontiers in Molecular Biosciences, 7, p.590165.
DOI -
Roy, R.,
Ghosh, B. and Kar, P., 2020.
Investigating conformational dynamics of Lewis Y oligosaccharides and elucidating blood group dependency of cholera using molecular dynamics.
ACS omega, 5(8), pp.3932-3942.
DOI
Full list available on Google Scholar.