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  1. Poddar, S., Roy, R., & Kar, P. (2024). The conformational dynamics of Hepatitis C virus E2 glycoprotein with the increasing number of N-glycosylation unraveled by molecular dynamics simulations.  Journal of Biomolecular Structure and Dynamics

  2. Ursal, K. D., Sk, M. F., Mahapatra, S., Kar, P. (2024). Unlocking Secrets of Down Syndrome Associated DYRK1A with Computational Microscope: Exploring Phosphorylation-Driven Structural Dynamics. Physical Chemistry Chemical Physics (Submitted)

  3. Poddar, S., Mahapatra, S., Jonniya, N.A.,  Kar, P. (2024). Comparative study of molecular interactions between the attachment glycoprotein of Henipvirus and ephrin receptors via molecular dynamics simulations. Journal of Molecular Graphics and Modeling (Under Review) 

  4. Are, V., Roy, R., Dhanda, S., Tiwari, R., Neema, S., Sahu, N., Adithya, N.,  Kar, P. (2024). Sequence homology and in-silico approach predicting candidate targets for immune responses to Kyasanur forest disease virus (KFDV), Alkhumra hemorrhagic fever virus (ALKV), and Tick-borne encephalitis virus (TBEV).  Journal of Molecular Modeling (Under Review)

  5. Dash, S., Jonniya, N.A., Samanta, S., Nayak, D., Kar, P. (2023). In-silico screening of small molecules against Kyasanur forest Disease virus (KFDV) RNA-dependent-RNA-polymerase. Journal of Molecular Modeling (Submitted)

  6. Koirala, S., Samanta, S., Kar, P. (2024). Dynamic Insights into Dual Leucine Zipper Kinase (DLK): Identification of Potential Inhibitors against Neurodegenerative Diseases Using Computational Tools, ACS Chemical Neuroscience (Submitted)

  7. Sk, M. F., Samanta, S., Poddar, S., Kar, P. (2024). Microsecond dynamics of H10N7 influenza neuraminidase reveals the plasticity of loop regions and drug resistance due to the R292K mutation.  Journal of Computational Chemistry, 45(5), 247-263.

  8. Sk, M. F., Samanta, S., Poddar, S., Kar, P. (2024). Deciphering the molecular choreography of Janus kinase 2 inhibition via Gaussian accelerated molecular dynamics simulations: A dynamic odyssey. Journal of Computer-Aided Molecular Design, 38 (1), 1-21.

  9. Binoy, A.; Kothari, M.; Sahadevan, R.; Poddar, S.; Kar, P.; Sadhukhan, S. (2024). Protein S-palmitoylation is markedly inhibited by 4"-alkyl ether lipophilic derivatives of EGCG, the major green tea polyphenol: In vitro and in silico studies.  BBA Biomembranes, 1866(3), 184264.

  10. Jaiswal, A.; Roy, R.; Tamarkar, A.; Singh A.; Kar, P.; Kodgire, P. (2023). Activation-induced cytidine deaminase an antibody diversification enzyme interacts with chromatin modifier UBN1 in B-cells. Scientific Reports, 13(1), 19615.

  11. Kashyap, D., Koirala, S., Roy, R., Saini, V., Varshney, N., Bagde, P., Samanta, S., Kar, P., Jha, H.C. (2023). Computational insights into VacA toxin inhibition: Harnessing FDA approved antibiotics against Helicobacter pylori. Journal of Biomolecular Structure and Dynamics 

  12. Poddar, S., Roy, R., & Kar, P. (2023). Deciphering 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

  13. Singh, S., Ghosh, P., Roy, R., Behera, A., Sahadevan, R., Kar, P., Sadhukhan, S., Sonawane, A., (2024). "4"-Alkyl EGCG derivatives induce cytoprotective autophagy response by inhibiting EGFR in Glioblastoma cells. ACS Omega, 2024, 9, 2, 2286–2301.

  14. Kashyap, D., Roy, R., Varshney, N., Baral, B., Bagde, B., Kandpal, M., Kumar, S., Kar, P., Jha, H.C. (2023). 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

  15. Roy, R., Sk, M. F., Tanwar, O., & Kar, P. (2023). Computational studies indicated the effectiveness of human metabolites against SARS-CoV-2 main protease. Molecular Diversity, 27, 1587-1602.

  16. Zhang, Y., Liu, C., Li, P., Jia, H., Ju, H., Zhang, J., Ferreira, E., Samanta, S., Kar, P., Huang, B., Liu, X., Zhan, P. (2023). Development of chalcone-like derivatives and their biological and mechanistic investigations as novel influenza nuclear export inhibitors. European Journal of Medicinal Chemistry, 261, 115845.

  17. Naga, R., Poddar, S., Bhattacharjee, A., Kar, P., Bose, A., Mattaparthi, V., Mukherjee, O., Saha, S. (2023). Structural analysis of human ATE1 isoforms and their interactions with Arg-tRNAArg. Journal of Biomolecular Structure and Dynamics.

  18. Jonniya, N.A., Poddar, S., Mahapatra, S., Kar, P. (2023). Computer-aided affinity enhancement of a cross-reactive antibody against dengue virus envelope domain III. Cell Biochemistry and Biophysics, 81, 737-755.

  19. Poddar, S., Roy, R.; Bhutia, N. T.; Kar, P. (2023). Exploring the energetics of binding of inhibitors to enoyl-CoA hydratase EchA6 of Mycobacterium tuberculosis using molecular dynamics simulations and deep learning. Computational Biology and Chemistry (Submitted)

  20. Koirala, S., Roy, R., Samanta, S., Mahapatra, S., & Kar, P. (2023). Plant derived active compounds of ayurvedic neurological formulation, Saraswatarishta as a potential dual leucine zipper kinase inhibitor: An in-silico study. Journal of Biomolecular Structure and Dynamics

  21. Koirala, S., Samanta, S., Mahapatra, S., Ursal, K., Poddar, S., & Kar, P. (2023). Molecular level investigation for identifying potential inhibitors against thymidylate kinase of monkeypox through in-silico approaches. Journal of Biomolecular Structure and Dynamics

  22. Kashyap, D., Koirala, S., Bagde, P., Saini, V., Samanta, S., Kar, P., Jha, H.C. (2023). Prediction of Rab5B inhibitors through integrative in-silico techniques. Molecular Diversity

  23. Mahapatra, S., Jonniya, N.A., Koirala, S., & Kar, P. (2023). Molecular dynamics simulations reveal phosphorylation-induced conformational dynamics of the fibroblast growth factor receptor 1 kinase. Journal of Biomolecular Structure and Dynamics, 42(6).

  24. Mahapatra, S., Jonniya, N.A., Koirala, S., Ursal, K., & Kar, P. (2023). The FGF/FGFR signalling mediated anti-cancer drug resistance and therapeutic intervention. Journal of Biomolecular Structure and Dynamics, 41(22), 13509-13533.

  25. Samanta, S., Sk, M.F., Koirala, S., & Kar, P. (2023). Exploring molecular interactions of potential inhibitors against the spleen tyrosine kinase implicated in autoimmune disorders via virtual screening and molecular dynamics simulations. SAR and QSAR in Environmental Research, 34(11), 869-897.

  26. Sk, M. F.; Kar, P. (2022). Finding Inhibitors and Deciphering Inhibitor-induced Conformational Plasticity in the Janus Kinase via Multiscale Simulations. SAR and QSAR in Environmental Research, 33(11), 833-859.

  27. Kashyap, D.; Roy, R.; Kar, P.; 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), 4770-4785.

  28. Roy, R.; Poddar, S.; Sk, M. F.; Kar, P. (2023). Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: Insight from 20 microsecond long atomistic molecular dynamic simulations. Journal of Biomolecular Structure and Dynamics, 41(8), 3305-3320.

  29. Roy, R., Poddar, S., & Kar, P. (2022). Comparison of the conformational dynamics of an N-glycan in implicit and explicit solvents. Carbohydrate Research, 522, 108700.

  30. Jonniya, N. A.; Kar, P. (2022). Functional Loop dynamics and Characterization of the Inactive State of the NS2B-NS3 Dengue Protease due to Allosteric Inhibitor Binding. Journal of Chemical Information and Modeling, 62(16), 3800-3813.

  31. Roy, R., Sk, M. F., Jonniya, N. A., Poddar, S., & Kar, P. (2022). Finding Potent Inhibitors against SARS-CoV-2 Main Protease Through Virtual Screening, ADMET, and Molecular Dynamic Simulation Studies, Journal of Biomolecular Structure and Dynamics, 40(14), 6556-6568.

  32. Rehman, S.; Bishnoi, S.; Roy, R.; Kumari, A.; Jayakumar, H.; Gupta, S.; Kar, P.; Pattanayak, A., Nayak, D. (2022). Virus-like particles (VLPs) of VSV-G for packaging and delivery of theranostic agents. ACS Omega, 7(37), 32840-32848.

  33. Jakhmola, S.; Sk, M. F.; Chatterjee, A.; Jain, K.; Kar, P., Jha, H. C. (2022). Myelin protein antigenic epitopes presented by major histocompatibility complexes; driver to multiple sclerosis.Computers in Biology and Medicine, 148, 105856.

  34. Jaiswal, S.; Roy, R.; Dutta, S.; Kar, P., Joshi, A.; Nayak, D.; Gupta, S. (2022). Role of Doxorubicin on the Loading Efficiency of ICG within Silk Fibroin Nanoparticles. ACS Biomaterials Science & Engineering, 8(7), 3054-3065.

  35. Shankar, U., Jain, N., Mishra, S. K., Sk, M. F., Kar, P., & Kumar, A. (2022). Mining of Ebola virus genome for the construction of multi-epitope vaccine to combat its infection. Journal of Biomolecular Structure and Dynamics, 40(11), 4815-4831.

  36. Singh, S.; Sahadevan, R.; Roy, R.; Biswas, M.; Ghosh, P.; Kar, P.; Sonawane, A.; Sadhukhan, S. (2022). Structure-based design and synthesis of a novel long-chain 4"-alkyl ether derivative of EGCG as potent and selective EGFR inhibitor: In-vitro and in-silico studies. RSC Advances, 12, 17821-17836.

  37. Roy, R.; Jonniya, N. A.; Kar, P. (2022). Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study. Journal of Physical Chemistry B, 126(21), 3852-3866.

  38. Roy, R., Mishra, A., Poddar, S., Nayak, D., & 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), 2302-2315.

  39. Sk, M. F.; Jonniya, N. A.; Roy, R.; Kar, P. (2022). Phosphorylation-Induced Conformational Dynamics and Inhibition of Janus Kinase 1 by Suppressors of Cytokine Signaling 1. Journal of Physical Chemistry B, 126(17), 3224-3239.

  40. Jain, N; Sk, M. F.; Mishra, A; Kar, P., Kumar, A. (2022). Identification of novel Efflux pump inhibitors for Neisseria gonorrhoeae via multiple ligand-based pharmacophores, e-pharmacophore, molecular docking, density functional theory, and Molecular dynamics approaches. Computational Biology and Chemistry, 98, 107682.

  41. Roy, R.; Jonniya, N. A.; Sk, M. F.; 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, 852895.

  42. Sk, M. F.; Jonniya, N. A.; Roy, R.; Kar, P. (2022). Unraveling the Molecular Mechanism of Recognition of Selected Next Generation Anti-rheumatoid Arthritis Inhibitors by Janus Kinase 1. ACS Omega. 7(7), 6195–6209.

  43. Omkar, I.; Sk, M. F.; Jakhmola, S.; Jonniya, N. A.; Jha, H.; Kar, P. (2022). Decoding the host-parasite protein interactions involved in cerebral malaria through glares of molecular dynamics simulations. Journal of Physical Chemistry B, 126(2), 387–402.

  44. Jonniya, N. A.; Sk, M. F.; Roy, R.; 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), 63-87.

  45. Jonniya, N. A., Sk, M. F., & Kar, P. (2022). A comparative study of structural and conformational properties of WNK kinase isoforms bound to an inhibitor: insights from molecular dynamic simulations. Journal of Biomolecular Structure and Dynamics, 40(3), 1400-1415.

  46. Pyasi, S., Jonniya, N. A., Sk, M. F., Nayak, D., & Kar, P. (2022). Finding potential inhibitors against RNA-dependent RNA polymerase (RdRp) of Bovine Ephemeral Fever Virus (BEFV): An in-silico study. Journal of Biomolecular Structure and Dynamics, 40(20), 10403-10421.

  47. Roy, R.; Jonniya, N. A., Poddar, S.; Sk, M. F.; 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), 6038-6052.

  48. Sk, M. F.; S. R. Haridev.; Roy, R.; 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), 941-962.

  49. Jonniya, N. A., Zhang, J., Kar, P. (2021). Molecular mechanism of inhibiting WNK binding to OSR1 by targeting the allosteric pocket of the OSR1-CCT domain with potential antihypertensive inhibitors: An in silico study. Journal of Physical Chemistry B, 125(32), 9115-9129.

  50. Jakhmola, S.; Jonniya, N. A.; Sk, M. F.; Kumari, Rani, A.; Kar, P.; Jha, H. C. (2021). Identification of potential inhibitors against Epstein–Barr Virus Nuclear Antigen 1 (EBNA1): An insight from docking and molecular dynamic simulations. ACS Chemical Neuroscience, 12(16), 3060-3072.

  51. Masand, V., Sk, M. F., Kar, P., Rastija, V., & Zaki, M. E. A. (2021). Identification of Food Compounds as Inhibitors of SARS-CoV-2 Main Protease Using Molecular Docking and Molecular Dynamics Simulations. Chemometrics and Intelligent Laboratory Systems, 217, 104394.

  52. Jonniya, N. A., Sk, M. F., & Kar, P. (2021). Elucidating specificity of an allosteric inhibitor WNK476 among WNK isoforms using molecular dynamic simulations. Chemical Biology & Drug Design, 98(3), 405-420.

  53. Jonniya, N. A., Sk, M. F., & Kar, P. (2021). Characterizing allosteric inhibitor-induced inactive state in With-No-Lysine kinase 1 using Gaussian accelerated molecular dynamics simulations. Physical Chemistry Chemical Physics, 23, 7343-7358.

  54. Tanwar, O., Soni, A., Prajapat, P., Shivhare, T., Pandey, S., & Kar, P. (2021). Ethyl Pyruvate as a potential defense intervention against Cytokine storm in COVID-19, ACS Omega, 6(11), 7754–7760.

  55. Singh, S., Sk, M.F., Sonawane, A., Kar, P., Sadhukhan, S. (2020). Plant-derived natural polyphenols as potential antiviral drugs against SARS-CoV-2 via RNA‐dependent RNA polymerase (RdRp) inhibition: An in-silico analysis. Journal of Biomolecular Structure and Dynamics, 39(16), 6249-6264.

  56. Sk, M.F., Jonniya, N. A., & Kar, P. (2021). Exploring the energetic basis of binding of currently used drugs against HIV-1 subtype CRF01_AE protease via molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics, 39(16), 5892-5909.

  57. Thurakkal, L., Singh, S., Roy, R., Kar, P., Sadhukhan, S., & Porel, M. (2020). 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, 138193.

  58. Sk, M.F., Jonniya, N. A., Roy, R., Poddar, S., & 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, 590165.

  59. Sk, M.F., Roy, R., Jonniya, N. A., Poddar, S., & 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), 3649-3661.

  60. Roy, R., Ghosh, B., & Kar, P. (2020). Investigating Conformational Dynamics of Lewis Y Oligosaccharides and Elucidating Blood Group Dependency of Cholera Using Molecular Dynamics. ACS Omega, 5(8), 3932-3942.

  61. Sk, M. F., Roy, R., & Kar, P. (2020). 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.

  62. Jonniya, N. A., Sk, M. F., & Kar, P. (2019). Investigating Phosphorylation-Induced Conformational Changes in WNK1 Kinase by Molecular Dynamics Simulations. ACS Omega, 4(17), 17404-17416.

  63. Jonniya, N. A., & Kar, P. (2019). Investigating specificity of the anti-hypertensive inhibitor WNK463 against With-No-Lysine kinase family isoforms via multiscale simulations. Journal of Biomolecular Structure and Dynamics, 38(5), 1306-1321.

  64. Kar, P., & Feig, M. (2017). Hybrid all-atom/coarse-grained simulations of proteins by direct coupling of CHARMM and PRIMO force fields. Journal of chemical theory and computation, 13(11), 5753-5765.

  65. Memczak, H., Lauster, D., Kar, P., Di Lella, S., Volkmer, R., Knecht, V., Herrmann, A., Ehrentreich-Förster, E., Bier, F. F., & Stöcklein, W. F. M. (2016). Anti-hemagglutinin antibody derived lead peptides for inhibitors of influenza virus binding. PloS One, 11(7), e0159074.

  66. Sengupta, S., Lingnurkar, R., Carey, T. S., Pomaville, M., Kar, P., Feig, M., ... & Henry, R. W. (2015). The evolutionarily conserved C-terminal domains in the mammalian retinoblastoma tumor suppressor family serve as dual regulators of protein stability and transcriptional potency. Journal of Biological Chemistry, 290(23), 14462-14475.

  67. Kar, P., & Feig, M. (2014). Recent advances in transferable coarse-grained modeling of proteins. In Advances in protein chemistry and structural biology (Vol. 96, pp. 143-180). Academic Press.

  68. Kar, P., Gopal, S. M., Cheng, Y. M., Panahi, A., & Feig, M. (2014). Transferring the primo coarse-grained force field to the membrane environment: simulations of membrane proteins and helix-helix association. Journal of Chemical Theory and Computation, 10(8), 3459-3472.

  69. Kar, P., Gopal, S. M., Cheng, Y. M., Predeus, A., & Feig, M. (2013). PRIMO: a transferable coarse-grained force field for proteins. Journal of chemical theory and computation, 9(8), 3769-3788.

  70. Kar, P., Lipowsky, R., & Knecht, V. (2013). Importance of polar solvation and configurational entropy for design of antiretroviral drugs targeting HIV-1 protease. Journal of Physical Chemistry B, 117(19), 5793-5805.

  71. Kar, P., & Knecht, V. (2012). Energetics of mutation-induced changes in potency of lersivirine against HIV-1 reverse transcriptase. Journal of Physical Chemistry B, 116(22), 6269-6278.

  72. Kar, P., & Knecht, V. (2012). Mutation-induced loop opening and energetics for binding of tamiflu to influenza N8 neuraminidase. Journal of Physical Chemistry B, 116(21), 6137-6149.

  73. Kar, P., & Knecht, V. (2012). Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir. Journal of Computer-Aided Molecular Design, 26(2), 215-232.

  74. Kar, P., & Knecht, V. (2012). Origin of decrease in potency of darunavir and two related antiviral inhibitors against HIV-2 compared to HIV-1 protease. Journal of Physical Chemistry B, 116(8), 2605-2614.

  75. Kar, P., Lipowsky, R., & Knecht, V. (2012). Energetics of Cross-reactivity of Diels-Alderase Antibody 1E9 and its Variants with Steroids. From Computational Biophysics to Systems Biology (CBSB11)–Celebrating Harold Scheraga’s 90th Birthday, 8, 57.

  76. Kar, P., Lipowsky, R., & Knecht, V. (2011). Importance of polar solvation for cross-reactivity of antibody and its variants with steroids.  Journal of Physical Chemistry B, 115(23), 7661-7669.

  77. Kar, P., Nadler, W., & Hansmann, U. H. (2009). Microcanonical replica exchange molecular dynamics simulation of proteins. Physical Review E, 80(5), 056703.

  78. Kar, P., Seel, M., Weidemann, T., & Höfinger, S. (2009). Theoretical mimicry of biomembranes. FEBS Letters, 583(12), 1909-1915.

  79. Kar, P., Wei, Y., Hansmann, U. H., & Höfinger, S. (2007). Systematic study of the boundary composition in Poisson Boltzmann calculations. Journal of Computational Chemistry, 28(16), 2538-2544.

  80. Kar, P., Seel, M., Hansmann, U. H., & Höfinger, S. (2007). Dispersion Terms and Analysis of Size-and Charge Dependence in an Enhanced Poisson− Boltzmann Approach. Journal of Physical Chemistry B, 111(30), 8910-8918.

  81. Kar, P., Seel, M., Hansmann, U. H., & Hofinger, S. Comparing Semi-Empirical versus Classic Charge Assignments in BioMolecules and their Effect on Electrostatic Potentials. From Computational Biophysics to Systems Biology (CBSB07), 155.

  82. Kar, P., Seel, M., Hansmann, U. H., & Hofinger, S. Algorithmic Refinements to an Enhanced Poisson-Boltzmann Approach Used in Biomolecular Simulation. From Computational Biophysics to Systems Biology (CBSB07), 173.

  83. Kar, P., Wei, Y., Hansmann, U. H., & Höfinger, S. The Influence of Molecular Surface Composition on the Outcome of Poisson Boltzmann Calculations Performed to Obtain Solvation Free Energies. In NIC Workshop 2006 From Computational Biophysics to Systems Biology (p. 161).

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