Rupesh Agarwal
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View article: Blunt trauma causing thrombotic occlusive myocardial infarction
Blunt trauma causing thrombotic occlusive myocardial infarction Open
Introduction: Traumatic myocardial infarction (TMI) is a rare but serious complication of blunt chest trauma, typically arising from coronary artery dissection, intramural hematoma, or myocardial contusion. Early recognition and interventi…
View article: Sialic acid identity modulates host tropism of sialoglycan-binding viridans group streptococci
Sialic acid identity modulates host tropism of sialoglycan-binding viridans group streptococci Open
Microbial interactions with multiple species may expand the range of potential hosts, supporting both pathogen reservoirs and zoonotic spillover. Viridans group streptococci interact with host cells by engaging protein-attached glycosylati…
View article: Sialic Acid Identity Modulates Host Tropism of Sialoglycan-binding Viridans Group Streptococci
Sialic Acid Identity Modulates Host Tropism of Sialoglycan-binding Viridans Group Streptococci Open
Microbial interactions with multiple species may expand the range of potential hosts, supporting both pathogen reservoirs and zoonotic spillover. Viridans group streptococci interact with host cells by engaging protein-attached glycosylati…
View article: Structure-Based Design of Small-Molecule Inhibitors of Human Interleukin-6
Structure-Based Design of Small-Molecule Inhibitors of Human Interleukin-6 Open
Human Interleukin-6 (hIL-6) is a pro inflammatory cytokine that binds to its receptor, IL-6Rα followed by binding to gp130 and subsequent dimerization to form a hexamer signaling complex. A critical inflammation mediator, hIL-6 is associat…
View article: GPRC6A is a Potential Therapeutic Target for Metformin Regulation of Glucose Homeostasis in Mice
GPRC6A is a Potential Therapeutic Target for Metformin Regulation of Glucose Homeostasis in Mice Open
Understanding the mechanism of metformin actions in treating type 2 diabetes is limited by an incomplete knowledge of the specific protein targets mediating its metabolic effects. Metformin has structural similarities to L-Arginine (2-amin…
View article: Osteocalcin binds to a <scp>GPRC6A</scp> Venus fly trap allosteric site to positively modulate <scp>GPRC6A</scp> signaling
Osteocalcin binds to a <span>GPRC6A</span> Venus fly trap allosteric site to positively modulate <span>GPRC6A</span> signaling Open
GPRC6A, a member of the Family C G‐protein coupled receptors, regulates energy metabolism and sex hormone production and is activated by diverse ligands, including cations, L‐amino acids, the osteocalcin (Ocn) peptide and the steroid hormo…
View article: Structure-Based Identification of Novel Histone Deacetylase 4 (HDAC4) Inhibitors
Structure-Based Identification of Novel Histone Deacetylase 4 (HDAC4) Inhibitors Open
Histone deacetylases (HDACs) are important cancer drug targets. Existing FDA-approved drugs target the catalytic pocket of HDACs, which is conserved across subfamilies (classes) of HDAC. However, engineering specificity is an important goa…
View article: Comparative Assessment of Pose Prediction Accuracy in RNA–Ligand Docking
Comparative Assessment of Pose Prediction Accuracy in RNA–Ligand Docking Open
Structure-based virtual high-throughput screening is used in early-stage drug discovery. Over the years, docking protocols and scoring functions for protein-ligand complexes have evolved to improve the accuracy in the computation of bindin…
View article: Characterization and molecular simulation of lignin in Cyrene pretreatment of switchgrass
Characterization and molecular simulation of lignin in Cyrene pretreatment of switchgrass Open
Biomass-derived solvents have been proposed as a novel pathway in biorefining for the realization of biofuels and bioproducts derived from lignocellulosic biomass.
View article: Pose prediction accuracy in ligand docking to RNA
Pose prediction accuracy in ligand docking to RNA Open
Structure-based virtual high-throughput screening is used in early-stage drug discovery. Over the years, docking protocols and scoring functions for protein-ligand complexes have evolved to improve accuracy in the computation of binding st…
View article: SARS-CoV2 billion-compound docking
SARS-CoV2 billion-compound docking Open
This dataset contains ligand conformations and docking scores for 1.4 billion molecules docked against 6 structural targets from SARS-CoV2, representing 5 unique proteins: MPro, NSP15, PLPro, RDRP, and the Spike protein. Docking was carrie…
View article: Speed vs Accuracy: Effect on Ligand Pose Accuracy of Varying Box Size and Exhaustiveness in AutoDock Vina
Speed vs Accuracy: Effect on Ligand Pose Accuracy of Varying Box Size and Exhaustiveness in AutoDock Vina Open
Structure‐based virtual high‐throughput screening involves docking chemical libraries to targets of interest. A parameter pertinent to the accuracy of the resulting pose is the root mean square deviation (RMSD) from a known crystallographi…
View article: Structure-based identification of novel histone deacetylase 4 (HDAC4) inhibitors
Structure-based identification of novel histone deacetylase 4 (HDAC4) inhibitors Open
Histone deacetylases (HDACs) are important cancer drug targets. Existing FDA-approved drugs target the catalytic pocket of HDACs, which is conserved across subfamilies (classes) of HDAC. Here, we use molecular modeling approaches to identi…
View article: Origins of glycan selectivity in streptococcal Siglec-like adhesins suggest mechanisms of receptor adaptation
Origins of glycan selectivity in streptococcal Siglec-like adhesins suggest mechanisms of receptor adaptation Open
View article: Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor
Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor Open
Inhibition of the SARS-CoV-2 main protease (Mpro) is a major focus of drug discovery efforts against COVID-19. Here we report a hit expansion of non-covalent inhibitors of Mpro. Starting from a recently discovered sca…
View article: Revised Glycemic Index for Diagnosing and Monitoring of Diabetes Mellitus in South Indian Population
Revised Glycemic Index for Diagnosing and Monitoring of Diabetes Mellitus in South Indian Population Open
Our population-based data indicate that for the South Indian population HbA1c value of ≥63 % and FPG value of ≥6.17 mmol/L may be optimal for diagnosing DM with a high level of accuracy and will be useful for the identification of mild and…
View article: Osteocalcin binds to a GPRC6A Venus fly trap allosteric site to positively modulate GPRC6A signaling
Osteocalcin binds to a GPRC6A Venus fly trap allosteric site to positively modulate GPRC6A signaling Open
GPRC6A is a member of the Family C G-protein coupled receptors that is activated by cations, L-amino acids, the osteocalcin (Ocn) peptide, and testosterone. GPRC6A functions as a master regulator of energy metabolism and sex hormone produc…
View article: A Model for the Signal Initiation Complex Between Arrestin-3 and the Src Family Kinase Fgr
A Model for the Signal Initiation Complex Between Arrestin-3 and the Src Family Kinase Fgr Open
View article: COVID-19 induced ventricular tachycardia storm unmasking a clinically silent cardiomyopathy: a case report
COVID-19 induced ventricular tachycardia storm unmasking a clinically silent cardiomyopathy: a case report Open
Background Coronavirus disease (COVID-19) is a systemic illness characterized by raging impact of cytokine storm on multiple organs. This may trigger malignant ventricular arrhythmias and unmask a clinically silent cardiomyopathy. Case sum…
View article: Cross-reactive immunogenicity of group A streptococcal vaccines designed using a recurrent neural network to identify conserved M protein linear epitopes
Cross-reactive immunogenicity of group A streptococcal vaccines designed using a recurrent neural network to identify conserved M protein linear epitopes Open
View article: Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19 Open
We present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protei…
View article: GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer
GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer Open
Protein-ligand docking is an in silico tool used to screen potential drug\ncompounds for their ability to bind to a given protein receptor within a\ndrug-discovery campaign. Experimental drug screening is expensive and time\nconsuming, and…
View article: Structure based virtual screening identifies small molecule effectors for the sialoglycan binding protein Hsa
Structure based virtual screening identifies small molecule effectors for the sialoglycan binding protein Hsa Open
Infective endocarditis (IE) is a cardiovascular disease often caused by bacteria of the viridans group of streptococci, which includes Streptococcus gordonii and Streptococcus sanguinis. Previous research has found that serine-rich repeat …
View article: Molecular dynamics analysis of the binding of human interleukin‐6 with interleukin‐6 <scp>α‐receptor</scp>
Molecular dynamics analysis of the binding of human interleukin‐6 with interleukin‐6 <span>α‐receptor</span> Open
Human interleukin‐6 (hIL‐6) is a multifunctional cytokine that regulates immune and inflammatory responses in addition to metabolic and regenerative processes and cancer. hIL‐6 binding to the IL‐6 receptor (IL‐6Rα) induces homodimerization…
View article: Konsenserfahrung von International Uveitis Study Group, Intraocular Inflammation Society und Foster Ocular Inflammation Society zur Uveitis in der Zeit der COVID-19-Infektion
Konsenserfahrung von International Uveitis Study Group, Intraocular Inflammation Society und Foster Ocular Inflammation Society zur Uveitis in der Zeit der COVID-19-Infektion Open
Zusammenfassung Dieses Dokument fasst die Erfahrungen der International Uveitis Study Group (IUSG), der Intraocular Inflammation Society (IOIS) und der Foster Ocular Inflammation Society (FOIS) zusammen und kann als Leitfaden für die Behan…
View article: Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19 Open
We present a supercomputer-driven pipeline for in-silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. We also describe preliminary results obtained for 23 systems involving eight protein targe…
View article: Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19 Open
We present a supercomputer-driven pipeline for in-silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. We also describe preliminary results obtained for 23 systems involving eight protein targets of t…
View article: GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research
GPU-Accelerated Drug Discovery with Docking on the Summit Supercomputer: Porting, Optimization, and Application to COVID-19 Research Open
Protein-ligand docking is an in silico tool used to screen potential drug compounds for their ability to bind to a given protein receptor within a drug-discovery campaign. Experimental drug screening is expensive and time consuming, and it…
View article: Mesophilic Pyrophosphatase Function at High Temperature: A Molecular Dynamics Simulation Study
Mesophilic Pyrophosphatase Function at High Temperature: A Molecular Dynamics Simulation Study Open
View article: Concurrent presence of retinal hemorrhages in the setting of acute Vogt-Koyanagi-Harada syndrome - an unusual presentation
Concurrent presence of retinal hemorrhages in the setting of acute Vogt-Koyanagi-Harada syndrome - an unusual presentation Open