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the literature.

peer-reviewed journal articles across computational biophysics, molecular recognition, glycobiology, and structural biology.

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2024

08 articles

01
Kashyap, D., Koirala, S., Roy, R., Saini, V., Varshney, N., Bagde, P. H., Samanta, S., Kar, P. and Jha, H. C.
Computational insights into VacA toxin inhibition: harnessing FDA-approved antibiotics against Helicobacter pylori
Journal of Biomolecular Structure and Dynamics · 42(24), 13725–13737
DOI
02
Poddar, S., Roy, R. and Kar, P.
Elucidating the conformational dynamics of histo-blood group antigens and their interactions with the rotavirus spike protein through a computational lens
Journal of Biomolecular Structure and Dynamics · 42(23), 13201–13215
DOI
03
Kashyap, D., Roy, R., Varshney, N., Baral, B., Bagde, P. H., Kandpal, M., Kumar, S., Kar, P. and Jha, H. C.
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), 9399–9415
DOI
04
Koirala, S.#, Roy, R.#, Samanta, S., Mahapatra, S. and Kar, P.
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), 11201–11214
DOI
05
Mukherjee, A., Paul, A., Roy, R. and Ghosh, K.
The role of extrinsic and intrinsic factors in perceptual filling-in of the blind-spot with variegated color and texture stimuli
Vision Research · 222, 108452
DOI
06
Are, V. N., Roy, R., Dhanda, S. K., Neema, S., Sahu, N. R., Adithya, N., Tiwari, R., Kar, P. and Nayak, D.
Predicting immune response targets in orthoflaviviruses through sequence homology and computational analysis
Journal of Molecular Modeling · 30(8), 295
DOI
07
Poddar, S., Roy, R. and Kar, P.
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 · 1–16
DOI
08
Singh, S., Ghosh, P., Roy, R., Behera, A., Sahadevan, R., Kar, P., Sadhukhan, S. and Sonawane, A.
4″-Alkyl EGCG derivatives induce cytoprotective autophagy response by inhibiting EGFR in glioblastoma cells
ACS Omega · 9(2), 2286–2301
DOI

2023

04 articles

01
Jaiswal, A., Roy, R., Tamrakar, A., Singh, A. K., Kar, P. and Kodgire, P.
Activation-induced cytidine deaminase, an antibody diversification enzyme, interacts with chromatin modifier UBN1 in B-cells
Scientific Reports · 13(1), 19615
DOI
02
Roy, R., Sk, M. F., Tanwar, O. and Kar, P.
Computational studies indicated the effectiveness of human metabolites against SARS-CoV-2 main protease
Molecular Diversity · 27(4), 1587–1602
DOI
03
Kashyap, D.#, Roy, R.#, Kar, P. and Jha, H. C.
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
DOI
04
Roy, R., Poddar, S., Sk, M. F. and Kar, P.
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), 3305–3320
DOI

2022

11 articles

01
Roy, R., Poddar, S. and Kar, P.
Comparison of the conformational dynamics of an N-glycan in implicit and explicit solvents
Carbohydrate Research · 522, 108700
DOI
02
Roy, R., Sk, M. F., Jonniya, N. A., Poddar, S. and Kar, P.
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), 6556–6568
DOI
03
Rehman, S., Bishnoi, S., Roy, R., Kumari, A., Jayakumar, H., Gupta, S., Kar, P., Pattnaik, A. K. and Nayak, D.
Emerging biomedical applications of the vesicular stomatitis virus glycoprotein
ACS Omega · 7(37), 32840–32848
DOI
04
Jaiswal, S., Roy, R., Dutta, S. B., Bishnoi, S., Kar, P., Joshi, A., Nayak, D. and Gupta, S.
Role of doxorubicin on the loading efficiency of ICG within silk fibroin nanoparticles
ACS Biomaterials Science & Engineering · 8(7), 3054–3065
DOI
05
Roy, R., Jonniya, N. A. and Kar, P.
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), 3852–3866
DOI
06
Roy, R., Jonniya, N. A., Sk, M. F. and Kar, P.
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
DOI
07
Sk, M. F., Jonniya, N. A., Roy, R. and Kar, P.
Phosphorylation-induced conformational dynamics and inhibition of Janus Kinase 1 by suppressors of cytokine signaling 1
The Journal of Physical Chemistry B · 126(17), 3224–3239
DOI
08
Roy, R.#, Mishra, A.#, Poddar, S., Nayak, D. and Kar, P.
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
DOI
09
Sk, M. F., Jonniya, N. A., Roy, R. and Kar, P.
Unraveling the molecular mechanism of recognition of selected next-generation antirheumatoid arthritis inhibitors by Janus kinase 1
ACS Omega · 7(7), 6195–6209
DOI
10
Jonniya, N. A., Sk, M. F., Roy, R. and Kar, P.
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
DOI
11
Singh, S., Sahadevan, R., Roy, R., Biswas, M., Ghosh, P., Kar, P., Sonawane, A. and Sadhukhan, S.
Structure-based design and synthesis of a novel long-chain 4″-alkyl ether derivative of EGCG as a potent EGFR inhibitor: in vitro and in silico studies
RSC Advances · 12(28), 17821–17836
DOI

2021

05 articles

01
Roy, R., Jonniya, N. A., Poddar, S., Sk, M. F. and Kar, P.
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
DOI
02
Sk, M. F., Haridev, S., Roy, R. and Kar, P.
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
DOI
03
Sk, M. F., Roy, R., Jonniya, N. A., Poddar, S. and Kar, P.
Elucidating the 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
DOI
04
Sk, M. F., Roy, R. and Kar, P.
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
05
Thurakkal, L., Singh, S., Roy, R., Kar, P., Sadhukhan, S. and Porel, M.
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
DOI

2020

02 articles

01
Sk, M. F., Jonniya, N. A., Roy, R., Poddar, S. and Kar, P.
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
DOI
02
Roy, R., Ghosh, B. and Kar, P.
Investigating conformational dynamics of Lewis Y oligosaccharides and elucidating blood group dependency of cholera using molecular dynamics
ACS Omega · 5(8), 3932–3942
DOI

# Equal contribution. Publication details and DOI destinations were checked against authoritative journal and indexing records.

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Research inthe literature.

Computational insights into VacA toxin inhibition: harnessing FDA-approved antibiotics against Helicobacter pylori

Elucidating the conformational dynamics of histo-blood group antigens and their interactions with the rotavirus spike protein through a computational lens

Withania somnifera extract reduces gastric cancerous properties through inhibition of gankyrin in cellular milieu produced by Helicobacter pylori and Epstein Barr virus

Plant-derived active compounds of ayurvedic neurological formulation Saraswatharishta as a potential dual leucine zipper kinase inhibitor: an in-silico study

The role of extrinsic and intrinsic factors in perceptual filling-in of the blind-spot with variegated color and texture stimuli

Predicting immune response targets in orthoflaviviruses through sequence homology and computational analysis

The conformational dynamics of Hepatitis C Virus E2 glycoprotein with the increasing number of N-glycosylation unraveled by molecular dynamics simulations

4″-Alkyl EGCG derivatives induce cytoprotective autophagy response by inhibiting EGFR in glioblastoma cells

Activation-induced cytidine deaminase, an antibody diversification enzyme, interacts with chromatin modifier UBN1 in B-cells

Computational studies indicated the effectiveness of human metabolites against SARS-CoV-2 main protease

Plant-derived active compounds as a potential nucleocapsid protein inhibitor of SARS-CoV-2: an in-silico study

Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: insights from 20 μs long atomistic molecular dynamic simulations

Comparison of the conformational dynamics of an N-glycan in implicit and explicit solvents

Finding potent inhibitors against SARS-CoV-2 main protease through virtual screening, ADMET, and molecular dynamics simulation studies

Emerging biomedical applications of the vesicular stomatitis virus glycoprotein

Role of doxorubicin on the loading efficiency of ICG within silk fibroin nanoparticles

Effect of sulfation on the conformational dynamics of dermatan sulfate glycosaminoglycan: a Gaussian accelerated molecular dynamics study

Comparative structural dynamics of isoforms of Helicobacter pylori adhesin BabA bound to Lewis b hexasaccharide via multiple-replica molecular dynamics simulations

Phosphorylation-induced conformational dynamics and inhibition of Janus Kinase 1 by suppressors of cytokine signaling 1

Investigating the mechanism of recognition and structural dynamics of nucleoprotein–RNA complex from Peste des petits ruminants virus via Gaussian accelerated molecular dynamics simulations

Unraveling the molecular mechanism of recognition of selected next-generation antirheumatoid arthritis inhibitors by Janus kinase 1

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

Structure-based design and synthesis of a novel long-chain 4″-alkyl ether derivative of EGCG as a potent EGFR inhibitor: in vitro and in silico studies

Unraveling the molecular mechanism of recognition of human interferon-stimulated gene product 15 by coronavirus papain-like proteases: a multiscale simulation study

Investigating potency of TMC-126 against wild-type and mutant variants of HIV-1 protease: a molecular dynamics and free energy study

Elucidating the biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations

Exploring the potency of currently used drugs against HIV-1 protease of subtype D variant by using multiscale simulations

An in-silico study on selected organosulfur compounds as potential drugs for SARS-CoV-2 infection via binding multiple drug targets

Computational investigation of structural dynamics of SARS-CoV-2 methyltransferase-stimulatory factor heterodimer nsp16/nsp10 bound to the cofactor SAM

Investigating conformational dynamics of Lewis Y oligosaccharides and elucidating blood group dependency of cholera using molecular dynamics

Research in
the literature.