Publications

Peer-Reviewed Journals

†equal contribution; * corresponding author

32. Ursal, Kapil; Sk, Md Fulbabu; Mahapatra, Subhasmita; Kar, Parimal* Unlocking the Conformational Secrets of DYRK1A Kinase with Computational Microscope: Exploring Phosphorylation-Driven Structural Dynamics, Journal of Computational Chemistry, 46(17), (2025), e70172 .

31.     Srivastava, Dushyant; Navratna, Vikas; Tosh, Dilip K.; Chinn, Audrey; Sk, Md Fulbabu; Tajkhorshid, Emad; Jacobson, Kenneth A.; Gouaux, Eric* Structure of the human dopamine transporter and mechanisms of allosteric inhibition, Nature, 632, (2024), 672–677.

30.     S. Samanta†; Sk, Md Fulbabu†; et al., Dynamic Interplay of Loop Motions Governs the Molecular Level Regulatory Dynamics in Spleen Tyrosine Kinase: Insights from Molecular Dynamics Simulations, Journal of Physical Chemistry B, 128(43), (2024), 10565-10580.

29.     Sk, Md Fulbabu; S. Samanta; S. Poddar; Kar, Parimal*, 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(8), 2024.

28.     Sk, Md Fulbabu; S. Samanta; Poddar, S; Kar, Parimal*, 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, (2024), 247-263.

27.     Roy, Rajarshi; Poddar, Sayan; Sk, Md Fulbabu; Kar, Parimal*, 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), (2023), 3305-3320.

26.     S. Samanta†; Md Fulbabu Sk†; et al.,Exploring molecular interactions of potential inhibitors against the Spleen Tyrosine Kinase implicated in Autoimmune disorders, SAR and QSAR in Environmental Research, 34(11), (2023), 869-897.

25.     Roy, Rajarshi†., Sk, Md Fulbabu†, Tanwar, O., Kar, Parimal*, Computational studies indicated the effectiveness of human metabolites against SARS-CoV-2 main protease, Molecular Diversity, 27(4), (2023), 1587-1602.

24.     Pyasi, Shruti; Jonniya, Nisha A.; Sk, Md Fulbabu; Nayak, Debasis*; Kar, Parimal, 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), (2022), 10403-1042.

23.     Sk, Md Fulbabu*; Kar, Parimal*, Finding inhibitors and deciphering inhibitor-induced conformational plasticity in the Janus Kinase via multiscale simulations, SAR and QSAR in Environmental Research. 33(11), (2022), 833-859.

22.  Sk, Md Fulbabu; Jonniya, N. A.; Roy, Rajarshi; Kar, Parimal*, Phosphorylation-induced conformational dynamics and inhibition of Janus kinase 1 by suppressors of cytokine signaling 1,  Journal of Physical Chemistry B, 126 (17), (2022), 3224-3239.

21.  Jakhmola, Shweta*†; Sk, Md Fulbabu†; Chatterjee, Akash; Jain, Khushboo; Kar, Parimal*, and Jha, Hem C.* A plausible contribution to multiple sclerosis; presentation of antigenic myelin protein epitopes by major histocompatibility complexes, Computers in Biology and Medicine, 148, (2022), 105865.

20.  Sk, Md Fulbabu; Jonniya, N. A.; Roy, Rajarshi; Kar, Parimal*, Unraveling the molecular mechanism of recognition of selected next generation antirheumatoid arthritis inhibitors by Janus kinase 1”. ACS Omega. 7(7), (2022), (6195-6209).

19.  Sk, Md Fulbabu†, Jonniya, Nisha A.†; Roy, Rajarshi; Poddar, Sayan; Kar, Parimal*, 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, (2020), 353.

18.  Roy, Rajarshi; Jonniya, Nisha A.; Sk, Md Fulbabu; Kar, Parimal*, Comparative structural dynamics of isoforms of Helicobacter pylori adhesin BabA bound to Lewisb hexasaccharide via multiple replica molecular dynamics simulations, Frontiers in Molecular Biosciences, 9, (2022), 852895.

17.   Indari, Omkar†; Sk, Md Fulbabu†; Jakhmola, Shweta.; Jonniya, Nisha A.; Jha, Hem*; Kar, Parimal*, “Decoding the host-parasite protein interactions involved in cerebral malaria through glares of molecular dynamics simulations, Journal of Physical Chemistry B. 126(2), (2022), 387-402.

16.  Jain, Neha*; Sk, Md Fulbabu; Mishra, Amit; Kar, Parimal; Kumar, Amit*, 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, (2022),107682.

15.  Jonniya, Nisha A.; Sk, Md Fulbabu; Roy, Rajarshi; Kar, Parimal*, 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), (2022), 63-87.

14.  Sk, Md Fulbabu; Roy, Rajarshi; Jonniya, Nisha A.; Poddar, Sayan; Kar, Parimal*, 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), (2021), 3649-3661.

13.  Sk, Md Fulbabu; Haridev, S. R.; Roy, Rajarshi; Kar, Parimal*, 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), (2021), 941-962.

12.  Sk, Md Fulbabu; Roy, Rajarshi; Kar, Parimal*, 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), (2021), 988-1003.

11.   Jonniya, Nisha A.; Sk, Md Fulbabu; Kar, Parimal*, Investigating phosphorylation-induced conformational changes in WNK1 kinase by molecular dynamics simulations, ACS omega, 4(17), (2019), 17404-17416.

10.  Sk, Md Fulbabu; Jonniya, Nisha A.; Kar, Parimal*, 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), (2021), 5892-5909.

9.  Jakhmola, Shweta; Jonniya, Nisha A.; Sk, Md Fulbabu; Rani, Annu; Kar, Parimal*; Jha, Hem C*, 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), (2021), 3060-3072.

8.  Roy, Rajarshi; Jonniya, Nisha A.; Poddar, Sayan; Sk, Md Fulbabu; Kar, Parimal*, 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), (2021), 6038-6052.

7.  Singh, Satyam; Sk, Md Fulbabu; Sonawane, Avinash; Kar, Parimal; Sadhukhan, Sushabhan*, 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), (2021), 6249-6266.

6.  Jonniya, Nisha A.; Sk, Md Fulbabu; Kar, Parimal*, Characterizing an allosteric inhibitor-induced inactive state in with-no-lysine kinase 1 using Gaussian accelerated molecular dynamics simulations, Physical Chemistry Chemical Physics, 23(12), (2021), 7343-7358.

5.  Jonniya, Nisha A.; Sk, Md Fulbabu; Kar, Parimal*, 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), (2022), 1400-1415.

4.  Jonniya, Nisha A.; Sk, Md Fulbabu; Kar, Parimal*, Elucidating specificity of an allosteric inhibitor WNK476 among With-No-Lysine kinase isoforms using molecular dynamic simulations, Chemical Biology & Drug Design, 98(3), (2021), 405-420.

3.  Roy, Rajarshi, Sk, Md Fulbabu, Jonniya, Nisha A.; Poddar, Sayan; Kar, Parimal*, 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), (2022), 6556-6568.

2.  Shankar, Uma; Jain, Neha; Mishra, Subodh K.; Sk, Md Fulbabu; Kar, Parimal; Kumar, Amit*, 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, (2022).

1.  Masand, Vijay H*; Sk, Md Fulbabu; Kar, Parimal; Vesna Rastija; Magdi EA. Zaki*, 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, (2021), 104394.