A. Roy

MDRepo - an open environment for data warehousing and knowledge discovery from molecular dynamics simulations

MDRepo provides an open repository for storing and analyzing molecular dynamics simulations to support drug discovery and structural biology research.

De Novo Design of Integrin α5β1 Modulating Proteins for Regenerative Medicine

The paper designs de novo proteins called NeoNectins that specifically bind integrin α5β1, enhancing cell attachment and tissue integration in biomaterials.

The Hidden Potential of PDE4 Inhibitor Rolipram: A Multifaceted Examination of its Inhibition of MMP2/9 Reveals Therapeutic Implications

This paper investigates rolipram's inhibition of MMP2/9 beyond its PDE4 activity, showing it affects MMP enzymatic activity and stability through direct protein binding.

Crosstalk between plasma membrane and Staphylococcus α-hemolysin during oligomerization

This study investigates the structural and functional dynamics of Staphylococcus aureus α-hemolysin during membrane interaction, revealing its role in cell necrosis and pore formation.

The Area Law of Molecular Entropy: Moving Beyond Harmonic Approximation.

This paper demonstrates that molecular thermodynamic entropy follows the area law with a correction for molecular surface curvature, enabling faster and more accurate entropy calculations than harmonic approximation methods.

Comparative metagenomic study unveils bacterial communities and their putative involvement in ecological success of two pine-feeding Ips beetle holobionts

This study compares bacterial communities in pine trees and two bark beetles before and after feeding, revealing life stage and environment effects on microbial associations.

Ready, set, yellow! Color Preference of Indian Free-ranging Dogs

This study investigates color preference in Indian free-ranging dogs, finding a strong preference for yellow over blue and gray, and yellow over food rewards.

DIRT/μ - Automated extraction of root hair traits using combinatorial optimization

DIRT/μ automatically extracts root hair traits from 2D images using combinatorial optimization, enabling precise and unbiased measurements of root hair length and density.

Mutation of a highly conserved isoleucine residue in loop 2 of several ????-coronavirus macrodomains indicates that enhanced ADP-ribose binding is detrimental to infection

This study shows that mutating a conserved isoleucine in the macrodomain of MERS-CoV and SARS-CoV-2 enhances ADP-ribose binding but reduces viral replication and pathogenesis.

A translation proofreader of archaeal origin imparts multialdehyde stress tolerance to land plants

This study shows that the archaeal DTD2 enzyme protects plants from aldehyde toxicity by removing harmful adducts on tRNA, and its overexpression enhances aldehyde resistance in Arabidopsis.

The IRE1α/XBP1 signaling axis drives myoblast fusion in adult skeletal muscle

This study shows that the IRE1α/XBP1 signaling pathway promotes myoblast fusion in skeletal muscle by upregulating profusion genes like Myomaker, crucial for muscle regeneration.

Transcriptomic response in pyroxsulam-resistant and susceptible Bromus sterilis identified three distinct mechanisms of resistance

The paper identifies three resistance mechanisms in pyroxsulam-resistant Bromus sterilis through transcriptomic analysis without ALS mutations.

De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8

This paper designs highly selective miniprotein inhibitors for integrins αvβ6 and αvβ8 with picomolar affinity and therapeutic potential in a mouse fibrosis model.

Combining phenotypic and genomic data to improve prediction of binary traits

The paper improves prediction of binary traits by combining genomic and phenotypic data using a two-step statistical method that prioritizes phenotypic variables.

Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments

This study identifies a molecular backdoor mechanism for inorganic phosphate release from actin filaments, showing how a disease-linked mutation alters Pi release rates and filament structure.

Transcription factor TFII-I fine tunes innate properties of B lymphocytes

This study shows that TFII-I is essential for maintaining innate B cell properties, with its loss causing myeloid-like transcriptomic changes and increased IgG3 switching.

Effects of microRNA-mediated negative feedback on gene expression noise

This study develops a mathematical model to show how miRNA-mediated negative feedback affects gene expression noise and creates bimodal mRNA distributions near an expression threshold.

Using evolutionary constraint to define novel candidate driver genes in medulloblastoma

The paper identifies novel candidate driver genes in medulloblastoma by analyzing non-coding constraint mutations across pediatric brain tumors and comparing them to benign tumors.

Do molecular fingerprints identify diverse active drugs in large-scale virtual screening? (no)

This study evaluates the effectiveness of molecular fingerprints in identifying active drugs during virtual screening and finds they lack discriminative power between active and inactive molecules.

HepT1-derived murine models of high-risk hepatoblastoma display vascular invasion, metastasis, and circulating tumor cells

This study develops murine hepatoblastoma models from HepT1 cells that exhibit high-risk features like vascular invasion, metastasis, and circulating tumor cells.

Impaired baroreceptor reflex sensitivity in pelvic suspension rats is associated with sympathovagal imbalance but not with carotid artery structural change

This study shows that 15 days of hindlimb unloading in rats reduces baroreflex sensitivity and heart rate variability, but does not cause structural changes in carotid arteries.

Temporal regulation of TAK1 to counteract muscular dystrophy

This study shows that regulating TAK1 activity can improve dystrophic muscle symptoms in a Duchenne muscular dystrophy mouse model.

The extracellular RNA pool within Zea mays apoplast: composition and differential expression during Ustilago maydis infection

The paper characterizes the extracellular RNA pool in maize apoplast under normal conditions and during Ustilago maydis infection, finding increased abundance and enrichment in ribosome biogenesis transcripts.

Protein kinase D promotes prostate cancer cell bone metastasis by positively regulating Runx2 in a MEK/ERK1/2-dependent manner

This study shows that PKD promotes prostate cancer bone metastasis by regulating Runx2 via MEK/ERK1/2 signaling, and inhibiting PKD reduces metastasis in mice.

Targeting an evolutionarily conserved "E-L-L" motif in the spike protein to develop a small molecule fusion inhibitor against SARS-CoV-2

This study identifies an evolutionarily conserved 'E-L-L' motif in the SARS-CoV-2 spike protein as a target for small molecule fusion inhibitors, showing posaconazole effectively blocks viral entry across variants.

Human bone marrow organoids for disease modelling, discovery and validation of therapeutic targets in hematological malignancies

This paper develops human bone marrow organoids to model hematological malignancies and validate therapeutic targets.

Discovery of small molecule inhibitors of Plasmodium falciparum apicoplast DNA polymerase

The paper screens small-molecule libraries to identify inhibitors of Plasmodium falciparum apicoplast DNA polymerase, finding nine potent compounds that inhibit parasite growth.

Uneven terrain treadmill walking in younger and older adults

This study tests how varying treadmill terrain unevenness affects gait kinematic variability and perceived stability in younger and older adults.

Discovery of compounds that inhibit SARS-CoV-2 Mac1-ADP-ribose binding by high-throughput screening

This study identifies 5 compounds that inhibit SARS-CoV-2 Mac1-ADP-ribose binding through high-throughput screening, with IC50 values under 100 µM.

Design, Synthesis and Evaluation of Inhibitors of the SARS-CoV-2 nsp3 Macrodomain

This study designs and synthesizes inhibitors targeting the SARS-CoV-2 nsp3 macrodomain, identifying compound 15c as a low-micromolar inhibitor with structural and thermal evidence of binding.