In silico
View article: Long Non-Coding RNAs Associated with Breast Cancer Cell Apoptosis Following Resveratrol Treatment: An In Silico Analysis
Long Non-Coding RNAs Associated with Breast Cancer Cell Apoptosis Following Resveratrol Treatment: An In Silico Analysis Open
Phytochemicals such as resveratrol accomplish their pleiotropic anti-tumor activities by modulating the expression of non-coding RNAs. This study examined the role of resveratrol in modulating long non-coding RNAs (lncRNAs) for apoptosis o…
View article: High F-Value Oligopeptides from Zanthoxylum bungeanum Seeds: Preparation Optimization and in Silico Screening of Xanthine Oxidase Inhibitory
High F-Value Oligopeptides from Zanthoxylum bungeanum Seeds: Preparation Optimization and in Silico Screening of Xanthine Oxidase Inhibitory Open
In this study, the optimal preparation conditions for high F-value oligopeptides from Zanthoxylum bungeanum seeds and xanthine oxidase (XOD) inhibitory were investigated. Based on the efficient enzymatic hydrolysis of Zanthoxylum bungeanum…
View article: Supplementary Figure S9 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer
Supplementary Figure S9 from Single-Cell Evolutionary Analysis Reveals Drivers of Plasticity and Mediators of Chemoresistance in Small Cell Lung Cancer Open
In silico removal and characterization of isolation of murine cells.
View article: Evaluation of Artificial Intelligence-Generated DNA Aptamers Against Treponema pallidum Surface Proteins
Evaluation of Artificial Intelligence-Generated DNA Aptamers Against Treponema pallidum Surface Proteins Open
DNA aptamer sequences were selected in silico with assistance from artificial intelligence (AI) using the new Xelari.com platform against three known immunogenic surface proteins of Treponema pallidum designated Tpp17, Tpp47 and Tp0751. Th…
View article: Conditional deep learning model reveals translation elongation determinants during amino acid deprivation
Conditional deep learning model reveals translation elongation determinants during amino acid deprivation Open
Translation elongation plays a key role in cellular homeostasis, and dysregulation of this process has been implicated in various diseases and metabolic disorders. Uncovering the causes of intragenic heterogeneity of translation, especiall…
View article: A Multidrug and Toxic Compound Extrusion Transporter, RgMATE6, Facilitates Vacuolar Transport of Acteoside in Rehmannia glutinosa
A Multidrug and Toxic Compound Extrusion Transporter, RgMATE6, Facilitates Vacuolar Transport of Acteoside in Rehmannia glutinosa Open
Acteoside (ACT), a prominent compound of the hydroxytyrosol-type phenylethanol glycoside (HPG) class, is present in plants and holds significant potential for food and pharmaceutical applications. However, the limited production of ACT in …
View article: Mechanism-informed identification of FDA-approved topoisomerase inhibitors disrupting SARS-CoV-2 nucleocapsid–RNA interactions
Mechanism-informed identification of FDA-approved topoisomerase inhibitors disrupting SARS-CoV-2 nucleocapsid–RNA interactions Open
View article: Cut or bind? Antigen-specific processing mechanisms define CD4+ T cell immunodominant epitopes for SARS-CoV-2 S and N proteins
Cut or bind? Antigen-specific processing mechanisms define CD4+ T cell immunodominant epitopes for SARS-CoV-2 S and N proteins Open
Background CD4⁺ T cell responses are key to adaptive immunity, yet the mechanisms underlying peptide selection and immunodominance across MHC class II variants in humans remain poorly defined. Two non-mutually exclusive models — First Bind…
View article: IN SILICO STUDY OF VANILLIN-DERIVTAIVES AS A GLUTAMATE RACEMASE (MurI) INHIBITORS
IN SILICO STUDY OF VANILLIN-DERIVTAIVES AS A GLUTAMATE RACEMASE (MurI) INHIBITORS Open
View article: metaTraits: a large-scale integration of microbial phenotypic trait information
metaTraits: a large-scale integration of microbial phenotypic trait information Open
Microbes differ greatly in their organismal structure, physiology, and environmental adaptation, yet information about these phenotypic traits is dispersed across multiple databases and is largely unavailable for taxa that remain unculture…
View article: Supplementary 1& 2: In Silico Structural and Functional Characterization of the HMPV M2-1 Protein Reveals Its Potential as a Therapeutic Target
Supplementary 1& 2: In Silico Structural and Functional Characterization of the HMPV M2-1 Protein Reveals Its Potential as a Therapeutic Target Open
Supplementary data
View article: In silico design of novel multi-epitope peptide vaccine against Neospora caninum induced cattle abortion targeting extracellular GRA2 and Nc-p43 protein
In silico design of novel multi-epitope peptide vaccine against Neospora caninum induced cattle abortion targeting extracellular GRA2 and Nc-p43 protein Open
Neospora caninum (NC) is a protozoan infection causing neosporosis, a disease that leads to substantial economic loss in livestock, especially in cattle, sheep, and goats. Unfortunately, there is presently no viable vaccination or authoriz…
View article: IN SILICO STUDY OF VANILLIN-DERIVTAIVES AS A GLUTAMATE RACEMASE (MurI) INHIBITORS
IN SILICO STUDY OF VANILLIN-DERIVTAIVES AS A GLUTAMATE RACEMASE (MurI) INHIBITORS Open
View article: In Silico Characterization of Conserved Epitopes in Alphavirus E2 Proteins: A Promising Approach for Pan-vaccine Design
In Silico Characterization of Conserved Epitopes in Alphavirus E2 Proteins: A Promising Approach for Pan-vaccine Design Open
View article: High-Throughput Fragment Screening Identifies a New Small Molecule Scaffold that Modulates TREM2 Signaling
High-Throughput Fragment Screening Identifies a New Small Molecule Scaffold that Modulates TREM2 Signaling Open
Fragment-based drug discovery (FBDD) remains a powerful tool in drug development for targeting a wide range of proteins and identifying new small molecule-based scaffolds. Here, we explored a fragment library of 3,200 compounds using a tem…
View article: Development and Use of Oral Microbiome Optimised Oxford Nanopore 16S Primers to Elucidate the Effect of Sialidase Inhibitors on a Plaque Community Biofilm Model
Development and Use of Oral Microbiome Optimised Oxford Nanopore 16S Primers to Elucidate the Effect of Sialidase Inhibitors on a Plaque Community Biofilm Model Open
The oral microbiome is a diverse ecosystem that plays a critical role in health and disease and contains numerous bacterial species capable of metabolizing host-derived glycans, particularly sialic acids. Sialidase enzymes can be produced …
View article: An Insight into Strain-Specificity of Streptomyces chrestomyceticus ADP4 and Identification of a Novel Peptide with Potential Antiviral Activities Against Significant Human Viruses, Including SARS-CoV2, HCV, and HIV
An Insight into Strain-Specificity of Streptomyces chrestomyceticus ADP4 and Identification of a Novel Peptide with Potential Antiviral Activities Against Significant Human Viruses, Including SARS-CoV2, HCV, and HIV Open
This study aimed to unravel the genomic uniqueness of Streptomyces chrestomyceticus ADP4 using whole-genome sequence analysis, with a focus on identifying strain-specific genes/proteins associated with a novel therapeutic source. The genom…
View article: Discovery of anti-inflammatory compounds from the stem bark of Garcinia latissima through in vitro and in silico approaches
Discovery of anti-inflammatory compounds from the stem bark of Garcinia latissima through in vitro and in silico approaches Open
Garcinia latissima Miq. has been traditionally used by local communities in Indonesia for wound healing and to relieve itching. A phytochemical investigation of the stem bark of G. latissima led to the isolation of 12 tocotrienol and trite…
View article: Micellangelo: a Generative Model of Cell-Topography Interactions
Micellangelo: a Generative Model of Cell-Topography Interactions Open
Understanding how materials influence cell behavior is central to biomaterial engineering, yet experimental approaches are limited by throughput and complexity. Here, we present Micellangelo, a generative AI model that simulates high-resol…
View article: Decoding the anti-inflammatory properties of sesquiterpene coumarins from the active fractions of Ferula assa-foetida through integrated experimental and in silico analyses
Decoding the anti-inflammatory properties of sesquiterpene coumarins from the active fractions of Ferula assa-foetida through integrated experimental and in silico analyses Open
Ferula assa-foetida known as Asafoetida has a long-established history in folk medicine as a therapeutically useful drug in many disorders. The current paper explored the in vivo and in vitro anti-inflammatory activities of the plant. Liqu…
View article: Genetic identification of the selenate reductase in <i>Enterobacter cloacae</i> SLD1a-1
Genetic identification of the selenate reductase in <i>Enterobacter cloacae</i> SLD1a-1 Open
Bacterial selenate reduction is a key microbial process that affects the speciation and mobility of selenium in the environment. In this study, we identified the selenate reductase gene in the facultative anaerobe Enterobacter cloacae SLD1…
View article: Figure S1 from Application of Novel Breast Biospecimen Cell-Type Adjustment Identifies Shared DNA Methylation Alterations in Breast Tissue and Milk with Breast Cancer–Risk Factors
Figure S1 from Application of Novel Breast Biospecimen Cell-Type Adjustment Identifies Shared DNA Methylation Alterations in Breast Tissue and Milk with Breast Cancer–Risk Factors Open
Correlation between estimated relative proportions of immune cells and true relative proportions in the in silico mixtures (n=12). Component cell types include B cells, CD4+ T cells, CD8+ T cells, monocytes, neutrophils, and NK cells.
View article: In Silico Design of Tweezer-like Molecules for the Specific Detection of Sucrose at Ultra Low Concentration
In Silico Design of Tweezer-like Molecules for the Specific Detection of Sucrose at Ultra Low Concentration Open
View article: Conversational no-code and multi-agentic disease module identification and drug repurposing prediction with ChatDRex
Conversational no-code and multi-agentic disease module identification and drug repurposing prediction with ChatDRex Open
Repurposing approved drugs offers a time-efficient and cost-effective alternative to traditional drug development. However, in silico prediction of repurposing candidates is challenging and requires the effective collaboration of specialis…
View article: Synthesis, structural elucidation, and molecular docking of diclofenac-derived hydrazone metal complexes with anti-inflammatory and anticancer potential
Synthesis, structural elucidation, and molecular docking of diclofenac-derived hydrazone metal complexes with anti-inflammatory and anticancer potential Open
A novel Schiff base ligand, (E)-2-(2-((2,6-dichlorophenyl)amino)phenyl)-N’-(2-hydroxynaphthalen-1-yl)methylene)acetohydrazide, was synthesized and complexed with Cu(II), Ni(II), Co(II), Gd(III), La(III), and Ag(I) ions. The resulting metal…
View article: A Globally Representative Immunopeptidomics Approach to Identify Population-Wide Vaccine Candidates
A Globally Representative Immunopeptidomics Approach to Identify Population-Wide Vaccine Candidates Open
Vaccine development has historically relied on preclinical testing using one or two cell lines, typically of Caucasian descent, contributing to vaccines that may fail to provide adequate protection across genetically diverse populations. A…
View article: Niosomal mefloquine and cisplatin in breast cancer: comparative effects on apoptosis and angiogenesis via in vitro and in silico analysis
Niosomal mefloquine and cisplatin in breast cancer: comparative effects on apoptosis and angiogenesis via in vitro and in silico analysis Open
The niosomal formulation of MEF synergistically enhances CIS efficacy by promoting apoptosis, and suppressing angiogenesis in TNBC. These findings highlight NMEF as a promising chemosensitizer to overcome cisplatin resistance. Future studi…
View article: An in silico study of the GCR1 role, mediated by Gibberellin GA1 and Abscisic Acid, to regulate GP in plant cells
An in silico study of the GCR1 role, mediated by Gibberellin GA1 and Abscisic Acid, to regulate GP in plant cells Open
View article: Immune Cell Type‐Specific DNA Methylation Regions Associate With 24‐Hour Blood Pressure Regulation in Black People
Immune Cell Type‐Specific DNA Methylation Regions Associate With 24‐Hour Blood Pressure Regulation in Black People Open
Background DNA methylation and immune cells have been linked to blood pressure (BP) regulation and the development of hypertension. However, the immune cell profiles and the cell type‐specific DNA methylation associated with BPs remain unc…
View article: Transcriptomic profiling of diabetic retinopathy: insights into RPL11 and bisphenol A
Transcriptomic profiling of diabetic retinopathy: insights into RPL11 and bisphenol A Open
Background Diabetic retinopathy (DR) is a leading microvascular complication of diabetes mellitus, causing irreversible vision loss in adults worldwide. However, the molecular mechanisms underlying DR pathogenesis—especially the crosstalk …