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Computational and Structural Biotechnology Journal
Scopus
ISSN 2001-0370 · American Association for the Advancement of Science (AAAS) · 3.623 artikel di indeks
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Artikel Jurnal
Prediction of protein-protein interactions using point transformer and spherical Convex Hull graphs
Accurate predictions and large-scale identification of protein-protein interactions (PPIs) are crucial for understanding their inherent biological mechanisms and protein functions in virtually all biological processes. Nowadays, graph-based deep learning models have made significant contributions…
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Network pharmacology of cellular targets in major depressive disorder and differential mechanisms of fluoxetine, ketamine and esketamine
Major depressive disorder (MDD) is a multifactorial mental health condition involving genetic, environmental, and neurobiological factors. Conventional antidepressants such as fluoxetine, a selective serotonin reuptake inhibitor, require weeks to exert therapeutic effects, whereas ketamine and…
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COVID-19 immunopathological features for the prediction and prevention of future emerging respiratory viral infections
Background & objective: Emerging viral infections can initiate a global pandemic with high mortality. Understanding the immunopathogenesis of these viruses is critical to developing effective strategies for managing/preventing such outbreaks. Methods: Transcriptomics analysis was performed in a UAE…
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Oxidative stress-driven transcriptomic remodeling in human astrocytes reveals network signatures associated with neurodegenerative and cardiovascular processes
Astrocytes are central to brain homeostasis, supporting neuronal metabolism, synaptic activity, and the blood–brain barrier. With aging, these glial cells undergo molecular and functional changes that weaken support functions and promote neuroinflammation, contributing to neurodegeneration. Yet the…
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Longitudinal omics data analysis: approaches and applications
Longitudinal omics data (LOD) analysis is essential for understanding the dynamics of biological processes and disease progression over time. This review explores various statistical and computational approaches for analyzing such data, emphasizing their applications and limitations. The main…
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Elucidating HER2-directed chimeric antigen receptor (CAR) activation mechanism using homology modeling and all-atom molecular dynamics simulation
HER2-directed chimeric antigen receptor (CAR) T cells have demonstrated robust in vivo cytotoxic activity against HER2-positive tumors. However, the structural basis of CAR activation and signal transduction across the membrane remains poorly defined due to the lack of full-length, high-resolution…
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Spliceosomal Sm core assembly: AlphaFold 3 predicted structure and phosphorylation-dependent regulation of the human 6S complex
The in vivo assembly of uridine-rich small nuclear ribonucleoproteins (U snRNPs), the central catalytic components of the spliceosome, is a highly organised, multi-step process orchestrated by several multi-protein complexes. Structural analyses have provided valuable insights into their overall…
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Hierarchical heated markov modeling for synthesizing activity data from wearable devices
Background: Wearable devices enable continuous acquisition of physiological and behavioral signals with broad utility in precision and population health. However, real-world datasets often have privacy constraints, irregular sampling, and activity-dependent recording, complicating data sharing and…
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Structural evolution of polymorphic class I HLA alleles, designating HLA-C with uncertain assemblies
Hyper polymorphic major histocompatibility class I (MHC) molecules are key components for acquired immune responses. They have high specificity towards peptides presented to CD8 + T cells, resembling vaccine design and autoimmunity. However, a broader landscape over such a diverse set of…
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A copula-infused graph neural network for cell type classification in single-cell RNA sequencing data
Cell-type classification from single-cell RNA sequencing (scRNA-seq) data is among the most important steps in understanding cellular heterogeneity and biological mechanisms. High dimensionality, sparsity, and noise in scRNA-seq data lead to significant computational and statistical challenges. To…
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Enhanced MiRISC expression noise reduction by self-feedback regulation of mRNA degradation
The microRNA (miRNA) induced silencing complex (miRISC) is the targeting apparatus and arguably the rate-limiting step of the miRNA-mediated regulatory subsystem – a major noise reducing, though metabolically costly, mechanism. Recently, we reported that miRISC channels miRNA-mediated regulatory…
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Mechanistic insights into dimerization and cross-β sheet formation in the HIV-associated amyloidogenic peptide PAP248–286 from unbiased all-atom molecular dynamics simulations
Semen-derived enhancer of viral infection (SEVI) fibrils, assembled from the peptide fragment PAP248–286, enhance HIV transmission by promoting viral attachment to host cells. However, the molecular basis of SEVI nucleation and early aggregation remains unclear. Here, we conducted 80 independent…
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Developing provider digital twins for personalized provider-patient communication via a RAG-based conversational framework
Digital twins have emerged as a paradigm in precision and personalized medicine, enabling data-driven modeling of individuals to support tailored interventions. While most existing work focuses on patient-oriented twins, little attention has been given to modeling the provider’s role, particularly…
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Bicuculline from Forsythia suspensa attenuates liver fibrosis via TLR4/MD2 inhibition and suppression of MyD88/NF-κB signaling
Liver fibrosis, a cardinal feature of chronic liver injury, involves hepatic stellate cells (HSCs) activation and excessive extracellular matrix (ECM) deposition. Upon liver fibrosis, TLR4 is highly expressed on HSCs and Kupffer cells. TLR4 activation induces liver inflammation followed by…
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Machine learning models for prediction of (Pro)cathepsin–glycosaminoglycan binding free energies based on molecular structure
Cathepsins are papain-like proteolytic enzymes localized in lysosomes and the extracellular matrix, where they participate in diverse physiological and pathological processes. They are synthesized as inactive precursors—procathepsins—containing a propeptide domain that blocks access to the active…
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Exploring transformer models: Fine-tuning VS inference on relation extraction from biomedical texts
Biomedical data continues to grow significantly, coming from different sources and being updated daily. This makes manual extraction not only time-consuming but also impossible to keep up with due to this constant increase. In this context, biomedical relation extraction, which aims to automate the…
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Trajectory-based computational analysis of the quantum–classical transition in asymmetrically coupled spin–boson models
Understanding how quantum coherence is regulated by structured environments is essential for elucidating energy-transfer mechanisms in photosynthetic light-harvesting complexes. In this work, we present a trajectory-based computational analysis of the quantum–classical transition in asymmetrically…
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Designing RNA sequencing experiments: A practical guide to reproducible gene expression analysis
RNA sequencing (RNA-seq) has become a cornerstone of modern biotechnology, offering a comprehensive and high-resolution view of gene expression that enables the discovery of novel transcripts across diverse biological systems. Its applications extend beyond basic transcriptomics, providing powerful…
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Computational and experimental insights into the interaction of the seaweed-derived steroidal metabolite 11α-hydroxyprogesterone with the glucocorticoid receptor
Seaweed-derived metabolites offer a rich source of bioactive compounds with therapeutic potential. In this study, 112 steroidal metabolites from Sargassum polycystum, Gracilaria fisheri, and Caulerpa lentillifera were computationally screened to identify candidates interacting with the…
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Artikel Jurnal
BioLogical: a universal analysis framework for biosystem logical dynamics
Complex biosystems exhibit ordered, functional, self-organized features, yet a universal framework for exploring their logical paradigms and dynamic behaviors remains lacking. Here we present BioLogical, a user-friendly R package designed to analyze logical properties of gene regulatory systems…
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