Yuguang Mu
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View article: Binding domains of α-synuclein receptors with monomeric/oligomeric α-synuclein: Implications for Parkinson’s disease
Binding domains of α-synuclein receptors with monomeric/oligomeric α-synuclein: Implications for Parkinson’s disease Open
Parkinson's disease (PD) and related synucleinopathies are characterized by the pathological aggregation and spread of alpha-synuclein (α-syn), a protein central to neurodegeneration. Currently three neuronal receptors -Family with sequenc…
View article: BridgeNet: a high-efficiency framework integrating sequence and structure for protein and enzyme function prediction
BridgeNet: a high-efficiency framework integrating sequence and structure for protein and enzyme function prediction Open
Understanding the relationship between protein sequences and structures is essential for accurate protein property prediction. We propose BridgeNet, a pre-trained deep learning framework that integrates sequence and structural information …
View article: Structures, Interactions, and Antimicrobial Activity of the Shortest Thanatin Peptide from Anasa tristis
Structures, Interactions, and Antimicrobial Activity of the Shortest Thanatin Peptide from Anasa tristis Open
Antimicrobial peptides (AMPs), also referred to as host defense peptides, are promising molecules in the development of the next generation of antibiotics against drug-resistant bacterial pathogens. Thanatin comprises a family of naturally…
View article: Giant Splitting of Folded Dirac Bands in Kekulé-ordered Graphene with Eu Intercalation
Giant Splitting of Folded Dirac Bands in Kekulé-ordered Graphene with Eu Intercalation Open
Kekulé-ordered graphene on SiC realized by intercalating two-dimensional metal layers offers a versatile platform for exploring intriguing quantum states and phenomena. Here, we achieve the intercalation of $(\mathrm{\sqrt{3}\times\sqrt{3}…
View article: Quantitative intra-Golgi transport and organization data suggest the stable compartment nature of the Golgi
Quantitative intra-Golgi transport and organization data suggest the stable compartment nature of the Golgi Open
How the intra-Golgi secretory transport works remains a mystery. The cisternal progression and the stable compartment models have been proposed and are under debate. Classic cisternal progression model posits that both the intra-Golgi tran…
View article: Quantitative intra-Golgi transport and organization data suggest the stable compartment nature of the Golgi
Quantitative intra-Golgi transport and organization data suggest the stable compartment nature of the Golgi Open
How the intra-Golgi secretory transport works remains a mystery. The cisternal progression and the stable compartment models have been proposed and are under debate. Classic cisternal progression model posits that both the intra-Golgi tran…
View article: scGAT: A Graph Attention Network Approach for Single-Cell Multi-Omics Data Analysis and Biomarker Discovery
scGAT: A Graph Attention Network Approach for Single-Cell Multi-Omics Data Analysis and Biomarker Discovery Open
Single-cell RNA sequencing (scRNA-seq) has transformed our understanding of cellular heterogeneity; however, many analytical methods focus on differential expression, overlooking intercellular interactions and disease progression. Here, we…
View article: <i>In silico</i> and <i>in vitro</i> mutational analysis to investigate the structure and pathogenicity of <i>POT1</i> missense variants
<i>In silico</i> and <i>in vitro</i> mutational analysis to investigate the structure and pathogenicity of <i>POT1</i> missense variants Open
We performed an initial assessment of 24 missense POT1variants using variant effect predictors (VEPs) followed by an extensive molecular dynamics (MD) simulations of 14 selected variants: N-terminal: I115T, Y223C, D224N, M251V, H266Q, and …
View article: Harnessing Cell Membrane-Derived Nanovesicles for Enhanced Nanoprobes in Multimodal Imaging: Progress and Perspectives
Harnessing Cell Membrane-Derived Nanovesicles for Enhanced Nanoprobes in Multimodal Imaging: Progress and Perspectives Open
Cell membrane-derived nanovesicles (CMNVs) are natural nanocarriers efficiently encapsulating bioactive molecules and imaging probes. Conventional nanoprobes face challenges, like rapid immune clearance, off-target accumulation, and long-t…
View article: Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction
Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction Open
The 3D structure of RNA critically influences its functionality, and understanding this structure is vital for deciphering RNA biology. Experimental methods for determining RNA structures are labour-intensive, expensive, and time-consuming…
View article: Single Disulfide Bond in Host Defense Thanatin Analog Peptides: Antimicrobial Activity, Atomic-Resolution Structures and Target Interactions
Single Disulfide Bond in Host Defense Thanatin Analog Peptides: Antimicrobial Activity, Atomic-Resolution Structures and Target Interactions Open
Host defense antimicrobial peptides (AMPs) are promising lead molecules with which to develop antibiotics against drug-resistant bacterial pathogens. Thanatin, an inducible antimicrobial peptide involved in the host defense of Podisus macu…
View article: Pharmacophore-guided de novo drug design with diffusion bridge
Pharmacophore-guided de novo drug design with diffusion bridge Open
De novo design of bioactive drug molecules with potential to treat desired biological targets is a profound task in the drug discovery process. Existing approaches tend to leverage the pocket structure of the target protein to condition th…
View article: Pharmacophore-guided de novo drug design with diffusion bridge
Pharmacophore-guided de novo drug design with diffusion bridge Open
De novo design of bioactive drug molecules with potential to treat desired biological targets is a profound task in the drug discovery process. Existing approaches tend to leverage the pocket structure of the target protein to condition th…
View article: Engineered Reactive Oxygen Species (ROS)‐Responsive Artificial H<sup>+</sup>/Cl<sup>−</sup> Ion Channels for Targeted Cancer Treatment
Engineered Reactive Oxygen Species (ROS)‐Responsive Artificial H<sup>+</sup>/Cl<sup>−</sup> Ion Channels for Targeted Cancer Treatment Open
Reactive oxygen species (ROS)‐responsive ion channels regulate the ion flow across the membranes in response to alterations in the cellular redox state, playing a crucial role in cellular adaptation to oxidative stress. Despite their signi…
View article: Discussion on health promotion behavior of patients with long COVID based on COM-B model and qualitative research on influencing factors
Discussion on health promotion behavior of patients with long COVID based on COM-B model and qualitative research on influencing factors Open
Objective To explore the health promotion behavior and its influencing factors of patients with long COVID, and to provide reference for the construction of intervention programs. Methods Totally 15 patients with long COVID were interviewe…
View article: Unraveling the molecular mechanism of <scp>FgGcn5</scp> inhibition by phenazine‐1‐carboxamide: combined <scp><i>in silico</i></scp> and <scp><i>in vitro</i></scp> studies
Unraveling the molecular mechanism of <span>FgGcn5</span> inhibition by phenazine‐1‐carboxamide: combined <span><i>in silico</i></span> and <span><i>in vitro</i></span> studies Open
BACKGROUND Fusarium head blight (FHB), mainly caused by Fusarium graminearum ( F . graminearum ), remains a devastating disease worldwide. The histone acetyltransferase Gcn5 plays a crucial role in epigenetic regulation. Aberrant Gcn5 acet…
View article: OpenDock: a pytorch-based open-source framework for protein–ligand docking and modelling
OpenDock: a pytorch-based open-source framework for protein–ligand docking and modelling Open
Motivation Molecular docking is an invaluable computational tool with broad applications in computer-aided drug design and enzyme engineering. However, current molecular docking tools are typically implemented in languages such as C++ for …
View article: Benchmarking reverse docking through <scp>AlphaFold2</scp> human proteome
Benchmarking reverse docking through <span>AlphaFold2</span> human proteome Open
Predicting the binding of ligands to the human proteome via reverse‐docking methods enables the understanding of ligand's interactions with potential protein targets in the human body, thereby facilitating drug repositioning and the evalua…
View article: Protein language models are performant in structure-free virtual screening
Protein language models are performant in structure-free virtual screening Open
Hitherto virtual screening (VS) has been typically performed using a structure-based drug design paradigm. Such methods typically require the use of molecular docking on high-resolution three-dimensional structures of a target protein—a co…
View article: Quantitative intra-Golgi transport and organization data suggest the stable compartment nature of the Golgi
Quantitative intra-Golgi transport and organization data suggest the stable compartment nature of the Golgi Open
How the intra-Golgi secretory transport works remains a mystery. The cisternal progression and the stable compartment models have been proposed and are under debate. Classic cisternal progression model posits that both the intra-Golgi tran…
View article: Protein language models are performant in structure-free virtual screening
Protein language models are performant in structure-free virtual screening Open
1.1 Abstract Hitherto virtual screening has been typically performed using a structure-based drug design paradigm. Such methods typically require the use of molecular docking on high-resolution three-dimensional structures of a target prot…
View article: Revealing the intricate mechanism governing the pH-dependent activity of a quintessential representative of flavoproteins, glucose oxidase
Revealing the intricate mechanism governing the pH-dependent activity of a quintessential representative of flavoproteins, glucose oxidase Open
Glucose oxidase (Gox), a prototypical flavoprotein, exhibits diverse industrial applications in glucose sensing and gluconic acid production. Its enzymatic activity is pH-dependent, with maximum activity observed at approximately neutral p…
View article: RmsdXNA: RMSD prediction of nucleic acid-ligand docking poses using machine-learning method
RmsdXNA: RMSD prediction of nucleic acid-ligand docking poses using machine-learning method Open
Small molecule drugs can be used to target nucleic acids (NA) to regulate biological processes. Computational modeling methods, such as molecular docking or scoring functions, are commonly employed to facilitate drug design. However, the a…
View article: A new paradigm for applying deep learning to protein–ligand interaction prediction
A new paradigm for applying deep learning to protein–ligand interaction prediction Open
Protein–ligand interaction prediction presents a significant challenge in drug design. Numerous machine learning and deep learning (DL) models have been developed to accurately identify docking poses of ligands and active compounds against…