Methodology-centered review of molecular modeling, simulation, and prediction of SARS-CoV-2

K Gao, R Wang, J Chen, L Cheng, J Frishcosy… - Chemical …, 2022 - ACS Publications
Despite tremendous efforts in the past two years, our understanding of severe acute
respiratory syndrome coronavirus 2 (SARS-CoV-2), virus–host interactions, immune …

[HTML][HTML] The exploration of phytocompounds theoretically combats SARS-CoV-2 pandemic against virus entry, viral replication and immune evasion

TH Chen, MJ Tsai, CS Chang, L Xu, YS Fu… - Journal of Infection and …, 2023 - Elsevier
Background The novel coronavirus disease-2019 (COVID-19) that emerged in China, is an
extremely contagious and pathogenic viral infection caused by the severe acute respiratory …

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… - Journal of Biomolecular …, 2023 - Taylor & Francis
Recent findings have highlighted the essential role of dual leucine zipper kinase (DLK) in
neuronal degeneration. Saraswatharishta (SWRT), an ayurvedic formulation utilized in …

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… - Journal of …, 2023 - Taylor & Francis
Abstract 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 …

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 …, 2023 - Taylor & Francis
Abstract The coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2. This virus
has a high mismatch repair proofreading ability due to its unique exonuclease activity …

Finding inhibitors and deciphering inhibitor-induced conformational plasticity in the Janus kinase via multiscale simulations

MF Sk, P Kar - SAR and QSAR in Environmental Research, 2022 - Taylor & Francis
The Janus kinase (JAK) is a master regulator of the JAK/STAT pathway. Dysregulation of this
signalling cascade causes neuroinflammation and autoimmune disorders. Therefore, JAKs …

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 …, 2022 - ACS Publications
The dysfunction of the JAK/STAT (Janus kinase/signal transducers and activators of
transcription) pathway results in several pathophysiological conditions, including …

[HTML][HTML] Comparative Structural Dynamics of Isoforms of Helicobacter pylori Adhesin BabA Bound to Lewis b Hexasaccharide via Multiple Replica Molecular …

R Roy, NA Jonniya, MF Sk, P Kar - Frontiers in Molecular Biosciences, 2022 - frontiersin.org
BabA of Helicobacter pylori is the ABO blood group antigen-binding adhesin. Despite
considerable diversity in the BabA sequence, it shows an extraordinary adaptation in …

Identification of inhibitors for neurodegenerative diseases targeting dual leucine zipper kinase through virtual screening and molecular dynamics simulations

S Koirala, S Samanta, P Kar - SAR and QSAR in Environmental …, 2024 - Taylor & Francis
Neurodegenerative diseases lead to a gradual decline in cognitive and motor functions due
to the progressive loss of neurons in the central nervous system. The role of dual leucine …

[HTML][HTML] 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… - Scientific Reports, 2023 - nature.com
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 …