Rajarshi Roy

Scopus Publications

The conformational dynamics of Hepatitis C Virus E2 glycoprotein with the increasing number of N-glycosylation unraveled by molecular dynamics simulations
Sayan Poddar, Rajarshi Roy, Parimal Kar
Journal of Biomolecular Structure and Dynamics, 2025
The Hepatitis C Virus (HCV), responsible for causing hepatitis and a significant contributor to liver disorders, presents a challenge for treatment due to its high genetic variability. Despite efforts, there is still no effective medication available for this virus. One of the promising targets for drug development involves targeting glycoprotein E2. However, our understanding of the dynamic behavior of E2 and its associated glycans remains limited. In this study, we investigated the dynamic characteristics of E2 with varying degrees of glycosylation using all-atom molecular dynamics simulations. We also explored glycan's interactions with the protein and among themselves. An overall increase in correlation between the vital protein regions was observed with an increase in glycan number. The protein dynamics is followed by the analysis of glycan dynamics, where the flexibility of the individual glycans was analyzed in their free and bound state, which revealed a decrease in their fluctuation in some cases. Furthermore, we generated the free energy landscape of individual N-glycan linkages in both free and bound states and observed both increases and decreases in flexibility, which can be attributed to the formation and breakage of hydrogen bonds with amino acids. Finally, we found that for a high glycosylation system, glycans interact with glycoprotein and form hydrogen bonds among themselves. Moreover, the hydrogen bond profiles of a given glycan can vary when influenced by other glycans. In summary, our study provides valuable insights into the dynamics of the core region of HCV E2 glycoprotein and its associated glycans.Communicated by Ramaswamy H. Sarma.
The role of extrinsic and intrinsic factors in perceptual filling-in of the blind-spot with variegated color and texture stimuli
Amrita Mukherjee, Avijit Paul, Rajarshi Roy, Kuntal Ghosh
Vision Research, 2024
Predicting immune response targets in orthoflaviviruses through sequence homology and computational analysis
Venkata N. Are, Rajarshi Roy, Sandeep Kumar Dhanda, Sanchit Neema, Neha Rani Sahu, et al.
Journal of Molecular Modeling, 2024
4″-Alkyl EGCG Derivatives Induce Cytoprotective Autophagy Response by Inhibiting EGFR in Glioblastoma Cells
Satyam Singh, Priya Ghosh, Rajarshi Roy, Ananyaashree Behera, Revathy Sahadevan, et al.
ACS Omega, 2024
Elucidating the conformational dynamics of histo-blood group antigens and their interactions with the rotavirus spike protein through computational lens
Sayan Poddar, Rajarshi Roy, Parimal Kar
Journal of Biomolecular Structure and Dynamics, 2024
In the present study, we investigated the conformational dynamics of histo-blood group antigens (HBGAs) and their interactions with the VP8* domain of four rotavirus genotypes (P[4], P[6], P[19], and P[11]) utilizing all-atom molecular dynamics simulations in explicit water. Our study revealed distinct changes in the dynamic behavior of the same glycan due to linkage variations. We observed that LNFPI HBGA having a terminal β linkage shows two dominant conformations after complexation, whereas only one was obtained for LNFPI with a terminal α linkage. Interestingly, both variants displayed a single dominant structure in the free state. Similarly, LNT and LNnT show a shift in their dihedral linkage profile between their two terminal monosaccharides because of a change in the linkage from β(1-3) to β(1-4). The molecular mechanics generalized Born surface area (MM/GBSA) calculations yielded the highest binding affinity for LNFPI(β)/P[6] (-13.93 kcal/mol) due to the formation of numerous hydrogen bonds between VP8* and HBGAs. LNnT binds more strongly to P[11] (-12.88 kcal/mol) than LNT (-4.41 kcal/mol), suggesting a single change in the glycan linkage might impact its binding profile significantly. We have also identified critical amino acids and monosaccharides (Gal and GlcNAc) that contributed significantly to the protein-ligand binding through the per-residue decomposition of binding free energy. Moreover, we found that the interaction between the same glycan and different protein receptors within the same rotavirus genogroup influenced the micro-level dynamics of the glycan. Overall, our study helps a deeper understanding of the H-type HBGA and rotavirus spike protein interaction.Communicated by Ramaswamy H. Sarma.
Plant derived active compounds of ayurvedic neurological formulation, Saraswatharishta as a potential dual leucine zipper kinase inhibitor: an in-silico study
Suman Koirala, Rajarshi Roy, Sunanda Samanta, Subhasmita Mahapatra, Parimal Kar
Journal of Biomolecular Structure and Dynamics, 2024
Recent findings have highlighted the essential role of dual leucine zipper kinase (DLK) in neuronal degeneration. Saraswatharishta (SWRT), an ayurvedic formulation utilized in traditional Indian medicine, has demonstrated effectiveness in addressing neurodegenerative diseases. Herein, we aim to delve into the atomistic details of the mode of action of phytochemicals present in SWRT against DLK. Our screening process encompassed over 500 distinct phytochemicals derived from the main ingredients of the SWRT formulation. Through a comparative analysis of docking scores and relative poses, we successfully identified four novel compounds, which underwent further investigation via 2 × 500 ns long molecular dynamics (MD) simulations. Among the top four compounds, CID16066851 sourced from the Acorus calamus displayed the most stable complex with DLK. The molecular mechanics Poisson - Boltzmann surface area (MM-PBSA) calculations highlighted the significance of electrostatic and van der Waals interactions in the binding recognition process. Additionally, we identified key residues, namely Phe192, Leu243, Val139, and Leu141, as hotspots that predominantly govern the DLK-inhibitor interaction. Notably, the leading compounds are sourced from the Acorus calamus, Syzygium aromaticum, Zingiber officinale, and Anethum sowa plants present in the SWRT formulation. Overall, the findings of our study hold promise for future drug development endeavors combating neurodegenerative conditions.Communicated by Ramaswamy H. Sarma.
Computational insights into VacA toxin inhibition: harnessing FDA-approved antibiotics against Helicobacter pylori
Dharmendra Kashyap, Suman Koirala, Rajarshi Roy, Vaishali Saini, Nidhi Varshney, et al.
Journal of Biomolecular Structure and Dynamics, 2024
Cancer is a condition in which a few of the body's cells grow beyond its control and spread to other outward regions. Globally, gastric cancer (GC) is third most common cause of cancer-related mortality and the fourth most common kind of cancer. Persistent infection of VacA-positive Helicobacter pylori (H. pylori) modulates cellular physiology and leads to GC. About ∼70% of H. pylori are positive for vacuolating cytotoxin-A (VacA), and it infects ∼80-90% of world populations. Herein, for first time, we repurposed FDA-approved gram-negative antibiotics, which are feasible alternatives to existing regimens and may be used in combinatorial treatment against VacA-positive H. pylori. Out of 110 FDA-approved antibiotics, we retrieved 92 structures, which were screened against the VacA protein. Moreover, we determined that the top eight hit antibiotics viz; cefpiramide, cefiderocol, eravacycline, doxycycline, ceftriaxone, enoxacin, tedizolid, and cefamandole show binding free energies of -9.1, -8.9, -8.1, -8.0, -7.9, -7.8, -7.8 and -7.8 Kcal/mol, respectively, with VacA protein. Finally, we performed 100 ns duplicate MD simulations on the top eight selected antibiotics showing strong VacA binding. Subsequently, five antibiotics, including cefiderocol, cefpiramide, doxycycline, enoxacin, and tedizolid show stable ligand protein distance and good binding affinity revealed by the MM-PBSA scheme. Among the five antibiotics cefiderocol act as the most potent inhibitor (-28.33 kcal/mol). Furthermore, we also identified the hotspot residue like Asn-506, Tyr-529, and Phe-483 which control the interaction. Concisely, we identified antibiotics that can be repurposed against VacA of H. pylori and explored their molecular mechanism of interaction with VacA.Communicated by Ramaswamy H. Sarma.
Withania somnifera extract reduces gastric cancerous properties through inhibition of gankyrin in cellular milieu produced by Helicobacter pylori and Epstein Barr virus
Dharmendra Kashyap, Rajarshi Roy, Nidhi Varshney, Budhadev Baral, Pranit Hemant Bagde, et al.
Journal of Biomolecular Structure and Dynamics, 2024
Helicobacter pylori and Epstein Barr virus (EBV) are group1 carcinogens and their role in Gastric cancer (GC) is well established. Previously we have shown that H. pylori and EBV appears to support aggressive gastric oncogenesis through the upregulation of oncoprotein Gankyrin. Natural plant active molecules have the potential to interrupt oncogenesis. Herein, we investigated the potential of Withania somnifera root extract (WSE) as a possible chemotherapeutic agent against host oncoprotein Gankyrin whose expression was altered by H. pylori and EBV-associated modified cellular milieu. The results show that WSE does not have any inhibitory effect on H. pylori and EBV-associated gene transcripts except for the lmps (lmp1, lmp2a, and lmp2B). Moreover, the WSE exert their anticancer activity via host cellular response and decreased the expression of cell-migratory (mmp3 and mmp7); cell-cycle regulator (pcna); antiapoptotic gene (bcl2); increased the expression of the proapoptotic gene (apaf1 and bax); and tumor suppressor (p53, prb, and pten). Knockdown of Gankyrin followed by the treatment of WSE also decreases the expression of TNF-ɑ, Akt, and elevated the expression of NFkB, PARP, Casp3, and Casp9. WSE also reduces cell migration, and genomic instability and forced the cells to commit programmed cell death. Moreover, molecular simulation studies revealed that out of eight active compounds of WSE, only four compounds such as withaferin A (WFA), withanoside IV (WA4), withanolide B (WNB), and withanolide D (WND) showed direct stable interaction with Gankyrin. This article reports for the first time that treatment of WSE decreased the cancerous properties through host cellular response modulation in gastric epithelial cells coinfected with H. pylori and EBV.Communicated by Ramaswamy H. Sarma.
Activation-induced cytidine deaminase an antibody diversification enzyme interacts with chromatin modifier UBN1 in B-cells
Ankit Jaiswal, Rajarshi Roy, Anubhav Tamrakar, Amit Kumar Singh, Parimal Kar, et al.
Scientific Reports, 2023
Activation-induced cytidine deaminase (AID) is the key mediator of antibody diversification in activated B-cells by the process of somatic hypermutation (SHM) and class switch recombination (CSR). Targeting AID to the Ig genes requires transcription (initiation and elongation), enhancers, and its interaction with numerous factors. Furthermore, the HIRA chaperon complex, a regulator of chromatin architecture, is indispensable for SHM. The HIRA chaperon complex consists of UBN1, ASF1a, HIRA, and CABIN1 that deposit H3.3 onto the DNA, the SHM hallmark. We explored whether UBN1 interacts with AID using computational and in-vitro experiments. Interestingly, our in-silico studies, such as molecular docking and molecular dynamics simulation results, predict that AID interacts with UBN1. Subsequently, co-immunoprecipitation and pull-down experiments established interactions between UBN1 and AID inside B-cells. Additionally, a double immunofluorescence assay confirmed that AID and UBN1 were co-localized in the human and chicken B-cell lines. Moreover, proximity ligation assay studies validated that AID interacts with UBN1. Ours is the first report on the interaction of genome mutator enzyme AID with UBN1. Nevertheless, the fate of interaction between UBN1 and AID is yet to be explored in the context of SHM or CSR.
Computational studies indicated the effectiveness of human metabolites against SARS-Cov-2 main protease
Rajarshi Roy, Md Fulbabu Sk, Omprakash Tanwar, Parimal Kar
Molecular Diversity, 2023
Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: Insights from 20 μs long atomistic molecular dynamic simulations
Rajarshi Roy, Sayan Poddar, Md Fulbabu Sk, Parimal Kar
Journal of Biomolecular Structure and Dynamics, 2023
Plant-derived active compounds as a potential nucleocapsid protein inhibitor of SARS-CoV-2: an in-silico study
Dharmendra Kashyap, Rajarshi Roy, Parimal Kar, Hem Chandra Jha
Journal of Biomolecular Structure and Dynamics, 2023
Comparison of the conformational dynamics of an N-glycan in implicit and explicit solvents
Rajarshi Roy, Sayan Poddar, Parimal Kar
Carbohydrate Research, 2022
Emerging Biomedical Applications of the Vesicular Stomatitis Virus Glycoprotein
Sheeba Rehman, Suman Bishnoi, Rajarshi Roy, Anshu Kumari, Harikrishnan Jayakumar, et al.
ACS Omega, 2022
Role of Doxorubicin on the Loading Efficiency of ICG within Silk Fibroin Nanoparticles
Saumya Jaiswal, Rajarshi Roy, Surjendu Bikash Dutta, Suman Bishnoi, Parimal Kar, et al.
ACS Biomaterials Science and Engineering, 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
Satyam Singh, Revathy Sahadevan, Rajarshi Roy, Mainak Biswas, Priya Ghosh, et al.
Rsc Advances, 2022
Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study
Rajarshi Roy, Nisha Amarnath Jonniya, Parimal Kar
Journal of Physical Chemistry B, 2022
Phosphorylation-Induced Conformational Dynamics and Inhibition of Janus Kinase 1 by Suppressors of Cytokine Signaling 1
Md Fulbabu Sk, Nisha Amarnath Jonniya, Rajarshi Roy, Parimal Kar
Journal of Physical Chemistry B, 2022
Comparative Structural Dynamics of Isoforms of Helicobacter pylori Adhesin BabA Bound to Lewis b Hexasaccharide via Multiple Replica Molecular Dynamics Simulations
Rajarshi Roy, Nisha Amarnath Jonniya, Md Fulbabu Sk, Parimal Kar
Frontiers in Molecular Biosciences, 2022
Unraveling the Molecular Mechanism of Recognition of Selected Next-Generation Antirheumatoid Arthritis Inhibitors by Janus Kinase 1
Md Fulbabu Sk, Nisha Amarnath Jonniya, Rajarshi Roy, Parimal Kar
ACS Omega, 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
N.A. Jonniya, M.F. Sk, R. Roy, P. Kar
SAR and QSAR in Environmental Research, 2022
Finding potent inhibitors against SARS-CoV-2 main protease through virtual screening, ADMET, and molecular dynamics simulation studies
Rajarshi Roy, Md Fulbabu Sk, Nisha Amarnath Jonniya, Sayan Poddar, Parimal Kar
Journal of Biomolecular Structure and Dynamics, 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
Rajarshi Roy, Anurag Mishra, Sayan Poddar, Debasis Nayak, Parimal Kar
Journal of Biomolecular Structure and Dynamics, 2022
Unraveling the Molecular Mechanism of Recognition of Human Interferon-Stimulated Gene Product 15 by Coronavirus Papain-Like Proteases: A Multiscale Simulation Study
Rajarshi Roy, Nisha Amarnath Jonniya, Sayan Poddar, Md Fulbabu Sk, Parimal Kar
Journal of Chemical Information and Modeling, 2021
An in-silico study on selected organosulfur compounds as potential drugs for SARS-CoV-2 infection via binding multiple drug targets
Liya Thurakkal, Satyam Singh, Rajarshi Roy, Parimal Kar, Sushabhan Sadhukhan, et al.
Chemical Physics Letters, 2021
Exploring the potency of currently used drugs against HIV-1 protease of subtype D variant by using multiscale simulations
Md Fulbabu Sk, Rajarshi Roy, Parimal Kar
Journal of Biomolecular Structure and Dynamics, 2021
Investigating potency of TMC-126 against wild-type and mutant variants of HIV-1 protease: a molecular dynamics and free energy study
M.F. Sk, S. Haridev, R. Roy, P. Kar
SAR and QSAR in Environmental Research, 2021
Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations
Md Fulbabu Sk, Rajarshi Roy, Nisha Amarnath Jonniya, Sayan Poddar, Parimal Kar
Journal of Biomolecular Structure and Dynamics, 2021
Computational Investigation of Structural Dynamics of SARS-CoV-2 Methyltransferase-Stimulatory Factor Heterodimer nsp16/nsp10 Bound to the Cofactor SAM
Md Fulbabu Sk, Nisha Amarnath Jonniya, Rajarshi Roy, Sayan Poddar, Parimal Kar
Frontiers in Molecular Biosciences, 2020
Investigating Conformational Dynamics of Lewis y Oligosaccharides and Elucidating Blood Group Dependency of Cholera Using Molecular Dynamics
Rajarshi Roy, Biplab Ghosh, Parimal Kar
ACS Omega, 2020
Perceptual filling-in of blind-spot for surrounding color gradient stimuli
Amrita Mukherjee, Avijit Paul, Rajarshi Roy, Shibsankar Roy, Kuntal Ghosh
Lecture Notes in Computer Science Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics, 2018

RECENT SCHOLAR PUBLICATIONS

The conformational dynamics of Hepatitis C Virus E2 glycoprotein with the increasing number of N -glycosylation unraveled by molecular dynamics simulations
S Poddar, R Roy, P Kar
Journal of Biomolecular Structure and Dynamics 43 (18), 10342-10357 , 2025
2025
Citations: 2
Computational insights into VacA toxin inhibition: harnessing FDA-approved antibiotics against Helicobacter pylori
D Kashyap, S Koirala, R Roy, V Saini, N Varshney, PH Bagde, S Samanta, ...
Journal of Biomolecular Structure and Dynamics 42 (24), 13725-13737 , 2024
2024
Citations: 5
Elucidating the conformational dynamics of histo-blood group antigens and their interactions with the rotavirus spike protein through computational lens
S Poddar, R Roy, P Kar
Journal of Biomolecular Structure and Dynamics 42 (23), 13201-13215 , 2024
2024
Withania somnifera extract reduces gastric cancerous properties through inhibition of gankyrin in cellular milieu produced by Helicobacter pylori and Epstein Barr …
D Kashyap, R Roy, N Varshney, B Baral, PH Bagde, M Kandpal, S Kumar, ...
Journal of Biomolecular Structure and Dynamics 42 (18), 9399-9415 , 2024
2024
Citations: 9
Plant derived active compounds of ayurvedic neurological formulation, Saraswatharishta as a potential dual leucine zipper kinase inhibitor: an in-silico study
S Koirala, R Roy, S Samanta, S Mahapatra, P Kar
Journal of Biomolecular Structure and Dynamics 42 (20), 11201-11214 , 2024
2024
Citations: 8
The role of extrinsic and intrinsic factors in perceptual filling-in of the blind-spot with variegated color and texture stimuli
A Mukherjee, A Paul, R Roy, K Ghosh
Vision Research 222, 108452 , 2024
2024
Citations: 1
Predicting immune response targets in orthoflaviviruses through sequence homology and computational analysis
VN Are, R Roy, SK Dhanda, S Neema, NR Sahu, N Adithya, R Tiwari, ...
Journal of Molecular Modeling 30 (8), 295 , 2024
2024
4 ″-Alkyl EGCG Derivatives Induce Cytoprotective Autophagy Response by Inhibiting EGFR in Glioblastoma Cells
S Singh, P Ghosh, R Roy, A Behera, R Sahadevan, P Kar, S Sadhukhan, ...
ACS omega 9 (2), 2286-2301 , 2024
2024
Citations: 6
Activation-induced cytidine deaminase an antibody diversification enzyme interacts with chromatin modifier UBN1 in B-cells
A Jaiswal, R Roy, A Tamrakar, AK Singh, P Kar, P Kodgire
Scientific Reports 13 (1), 19615 , 2023
2023
Citations: 6
Computational studies indicated the effectiveness of human metabolites against SARS-Cov-2 main protease
R Roy, MF Sk, O Tanwar, P Kar
Molecular Diversity 27 (4), 1587-1602 , 2023
2023
Citations: 7
Plant-derived active compounds as a potential nucleocapsid protein inhibitor of SARS-CoV-2: an in-silico study
D Kashyap, R Roy, P Kar, HC Jha
Journal of Biomolecular Structure and Dynamics 41 (10), 4770-4785 , 2023
2023
Citations: 12
Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: Insights from 20 μs long atomistic molecular dynamic simulations
R Roy, S Poddar, MF Sk, P Kar
Journal of Biomolecular Structure and Dynamics 41 (8), 3305-3320 , 2023
2023
Citations: 8
Asymmetric Perceptual Filling-In of Blind-Spot Through Novel Stimuli with Variegated Color and Texture Gradient
A Mukherjee, A Paul, R Roy, K Ghosh
Available at SSRN 4439324 , 2023
2023
Comparison of the conformational dynamics of an N-glycan in implicit and explicit solvents
R Roy, S Poddar, P Kar
Carbohydrate Research 522, 108700 , 2022
2022
Citations: 4
Finding potent inhibitors against SARS-CoV-2 main protease through virtual screening, ADMET, and molecular dynamics simulation studies
R Roy, MF Sk, NA Jonniya, S Poddar, P Kar
Journal of Biomolecular Structure and Dynamics 40 (14), 6556-6568 , 2022
2022
Citations: 25
Emerging biomedical applications of the vesicular stomatitis virus glycoprotein
S Rehman, S Bishnoi, R Roy, A Kumari, H Jayakumar, S Gupta, P Kar, ...
ACS omega 7 (37), 32840-32848 , 2022
2022
Citations: 13
Role of doxorubicin on the loading efficiency of ICG within silk fibroin nanoparticles
S Jaiswal, R Roy, SB Dutta, S Bishnoi, P Kar, A Joshi, D Nayak, S Gupta
ACS Biomaterials Science & Engineering 8 (7), 3054-3065 , 2022
2022
Citations: 12
Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study
R Roy, NA Jonniya, P Kar
The Journal of Physical Chemistry B 126 (21), 3852-3866 , 2022
2022
Citations: 15
Comparative Structural Dynamics of Isoforms of Helicobacter pylori Adhesin BabA Bound to Lewis b Hexasaccharide via Multiple Replica Molecular Dynamics …
R Roy, NA Jonniya, MF Sk, P Kar
Frontiers in Molecular Biosciences 9, 852895 , 2022
2022
Citations: 7
Phosphorylation-induced conformational dynamics and inhibition of Janus Kinase 1 by suppressors of cytokine signaling 1
MF Sk, NA Jonniya, R Roy, P Kar
The Journal of Physical Chemistry B 126 (17), 3224-3239 , 2022
2022
Citations: 10

MOST CITED SCHOLAR PUBLICATIONS

Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations
MF Sk, R Roy, NA Jonniya, S Poddar, P Kar
Journal of Biomolecular Structure and Dynamics 39 (10), 3649-3661 , 2021
2021
Citations: 92
Exploring the potency of currently used drugs against HIV-1 protease of subtype D variant by using multiscale simulations
MF Sk, R Roy, P Kar
Journal of Biomolecular Structure and Dynamics 39 (3), 988-1003 , 2021
2021
Citations: 48
An in-silico study on selected organosulfur compounds as potential drugs for SARS-CoV-2 infection via binding multiple drug targets
L Thurakkal, S Singh, R Roy, P Kar, S Sadhukhan, M Porel
Chemical physics letters 763, 138193 , 2021
2021
Citations: 48
Computational investigation of structural dynamics of SARS-CoV-2 methyltransferase-stimulatory factor heterodimer nsp16/nsp10 bound to the cofactor SAM
MF Sk, NA Jonniya, R Roy, S Poddar, P Kar
Frontiers in Molecular Biosciences 7, 590165 , 2020
2020
Citations: 48
Investigating conformational dynamics of Lewis Y oligosaccharides and elucidating blood group dependency of cholera using molecular dynamics
R Roy, B Ghosh, P Kar
ACS omega 5 (8), 3932-3942 , 2020
2020
Citations: 36
Investigating the mechanism of recognition and structural dynamics of nucleoprotein-RNA complex from Peste des petits ruminants virus via Gaussian accelerated …
R Roy, A Mishra, S Poddar, D Nayak, P Kar
Journal of Biomolecular Structure and Dynamics 40 (5), 2302-2315 , 2022
2022
Citations: 31
Finding potent inhibitors against SARS-CoV-2 main protease through virtual screening, ADMET, and molecular dynamics simulation studies
R Roy, MF Sk, NA Jonniya, S Poddar, P Kar
Journal of Biomolecular Structure and Dynamics 40 (14), 6556-6568 , 2022
2022
Citations: 25
Unraveling the molecular mechanism of recognition of selected next-generation antirheumatoid arthritis inhibitors by Janus kinase 1
MF Sk, NA Jonniya, R Roy, P Kar
ACS omega 7 (7), 6195-6209 , 2022
2022
Citations: 25
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
S Singh, R Sahadevan, R Roy, M Biswas, P Ghosh, P Kar, A Sonawane, ...
RSC advances 12 (28), 17821-17836 , 2022
2022
Citations: 24
Effect of Sulfation on the Conformational Dynamics of Dermatan Sulfate Glycosaminoglycan: A Gaussian Accelerated Molecular Dynamics Study
R Roy, NA Jonniya, P Kar
The Journal of Physical Chemistry B 126 (21), 3852-3866 , 2022
2022
Citations: 15
Emerging biomedical applications of the vesicular stomatitis virus glycoprotein
S Rehman, S Bishnoi, R Roy, A Kumari, H Jayakumar, S Gupta, P Kar, ...
ACS omega 7 (37), 32840-32848 , 2022
2022
Citations: 13
Plant-derived active compounds as a potential nucleocapsid protein inhibitor of SARS-CoV-2: an in-silico study
D Kashyap, R Roy, P Kar, HC Jha
Journal of Biomolecular Structure and Dynamics 41 (10), 4770-4785 , 2023
2023
Citations: 12
Role of doxorubicin on the loading efficiency of ICG within silk fibroin nanoparticles
S Jaiswal, R Roy, SB Dutta, S Bishnoi, P Kar, A Joshi, D Nayak, S Gupta
ACS Biomaterials Science & Engineering 8 (7), 3054-3065 , 2022
2022
Citations: 12
Unraveling the molecular mechanism of recognition of human interferon-stimulated gene product 15 by coronavirus papain-like proteases: A multiscale simulation study
R Roy, NA Jonniya, S Poddar, MF Sk, P Kar
Journal of Chemical Information and Modeling 61 (12), 6038-6052 , 2021
2021
Citations: 11
Phosphorylation-induced conformational dynamics and inhibition of Janus Kinase 1 by suppressors of cytokine signaling 1
MF Sk, NA Jonniya, R Roy, P Kar
The Journal of Physical Chemistry B 126 (17), 3224-3239 , 2022
2022
Citations: 10
Withania somnifera extract reduces gastric cancerous properties through inhibition of gankyrin in cellular milieu produced by Helicobacter pylori and Epstein Barr …
D Kashyap, R Roy, N Varshney, B Baral, PH Bagde, M Kandpal, S Kumar, ...
Journal of Biomolecular Structure and Dynamics 42 (18), 9399-9415 , 2024
2024
Citations: 9
Plant derived active compounds of ayurvedic neurological formulation, Saraswatharishta as a potential dual leucine zipper kinase inhibitor: an in-silico study
S Koirala, R Roy, S Samanta, S Mahapatra, P Kar
Journal of Biomolecular Structure and Dynamics 42 (20), 11201-11214 , 2024
2024
Citations: 8
Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: Insights from 20 μs long atomistic molecular dynamic simulations
R Roy, S Poddar, MF Sk, P Kar
Journal of Biomolecular Structure and Dynamics 41 (8), 3305-3320 , 2023
2023
Citations: 8
Computational studies indicated the effectiveness of human metabolites against SARS-Cov-2 main protease
R Roy, MF Sk, O Tanwar, P Kar
Molecular Diversity 27 (4), 1587-1602 , 2023
2023
Citations: 7
Comparative Structural Dynamics of Isoforms of Helicobacter pylori Adhesin BabA Bound to Lewis b Hexasaccharide via Multiple Replica Molecular Dynamics …
R Roy, NA Jonniya, MF Sk, P Kar
Frontiers in Molecular Biosciences 9, 852895 , 2022
2022
Citations: 7

Rajarshi Roy

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RECENT SCHOLAR PUBLICATIONS

MOST CITED SCHOLAR PUBLICATIONS