A5100451017- Protein Structure and Dynamics
- Computational Drug Discovery Methods
- Machine Learning in Materials Science
- SARS-CoV-2 and COVID-19 Research
- Machine Learning in Bioinformatics
- Enzyme Structure and Function
- Botanical Research and Chemistry
- Genomics and Phylogenetic Studies
- Viral Infections and Vectors
- Mass Spectrometry Techniques and Applications
- Mycobacterium research and diagnosis
- COVID-19 Clinical Research Studies
- AI in cancer detection
- Radiomics and Machine Learning in Medical Imaging
- Viral Infections and Outbreaks Research
- Bioinformatics and Genomic Networks
- RNA and protein synthesis mechanisms
- Tuberculosis Research and Epidemiology
- Video Surveillance and Tracking Methods
- Gene Regulatory Network Analysis
- Advanced Adaptive Filtering Techniques
- Plant Stress Responses and Tolerance
- Bacteriophages and microbial interactions
- Biomedical Text Mining and Ontologies
- Microbial Metabolites in Food Biotechnology
Microsoft Research Asia (China)
2021-2025
Wuhan Institute of Virology
2024
Chinese Academy of Sciences
2024
Huazhong University of Science and Technology
2022-2024
Tianjin Medical University
2024
Second Hospital of Tianjin Medical University
2024
Harbin Medical University
2024
Union Hospital
2022-2024
Dalian University of Technology
2023-2024
Peking Union Medical College Hospital
2020-2023
Abstract Geometric deep learning has been revolutionizing the molecular modeling field. Despite state-of-the-art neural network models are approaching ab initio accuracy for property prediction, their applications, such as drug discovery and dynamics (MD) simulation, have hindered by insufficient utilization of geometric information high computational costs. Here we propose an equivariant geometry-enhanced graph called ViSNet, which elegantly extracts features efficiently structures with low...
Peanut is an important oil crop worldwide and shows considerable adaptability but growth yield are negatively affected by continuous cropping. Soil micro-organisms efficient bio-indicators of soil quality plant health critical to the sustainability soil-based ecosystem function successful growth. In this study, 18S rRNA gene clone library analyses were employed study succession progress eukaryotic under peanut cultivation. Eight libraries constructed for over three cropping cycles its...
Drug-drug interaction (DDI) prediction identifies interactions of drug combinations in which the adverse side effects caused by physicochemical incompatibility have attracted much attention. Previous studies usually model information from single or dual views whole molecules but ignore detailed among atoms, leads to incomplete and noisy limits accuracy DDI prediction. In this work, we propose a novel dual-view representation learning network for ('DSN-DDI'), employs local global modules...
Biomolecular dynamics simulation is a fundamental technology for life sciences research, and its usefulness depends on accuracy efficiency
Machine learning force fields (MLFFs) have gained popularity in recent years as they provide a cost-effective alternative to ab initio molecular dynamics (MD) simulations. Despite small error on the test set, MLFFs inherently suffer from generalization and robustness issues during MD To alleviate these issues, we propose global metrics fine-grained element conformation aspects systematically measure for every atom of molecules. We selected three state-of-the-art (ET, NequIP, ViSNet)...
ABSTRACT Since SARS-CoV-2 Omicron variant (B.1.1.529) was reported in November 2021, it has quickly spread to many countries and outcompeted the globally dominant Delta several countries. The contains largest number of mutations date, with 32 located at spike (S) glycoprotein, which raised great concern for its enhanced viral fitness immune escape [1–4] . In this study, we crystal structure receptor binding domain (RBD) S glycoprotein bound human ACE2 a resolution 2.6 Å. Structural...
Abstract Molecular dynamics (MD) simulations have revolutionized the modeling of biomolecular conformations and provided unprecedented insight into molecular interactions. Due to prohibitive computational overheads ab initio simulation for large biomolecules, dynamic proteins is generally constrained on force field with mechanics, which suffers from low accuracy as well ignores electronic effects. Here, we report AIMD-Chig, an MD dataset including 2 million 166-atom protein Chignolin sampled...
Abstract Phormium tenax is a kind of drought resistant garden plant with its rich and colorful leaves. To clarify the molecular mechanism resistance in , transcriptome was sequenced by Illumina sequencing technology under normal stress, respectively. A large number contigs, transcripts unigenes were obtained. Among them, only 30,814 annotated comparing protein databases. total 4,380 genes differentially expressed, 2,698 which finally stress. Differentially expression analysis also performed...
SARS-CoV-2 is what has caused the COVID-19 pandemic. Early viral infection mediated by homo-trimeric Spike (S) protein with its receptor binding domains (RBDs) in receptor-accessible state. Molecular dynamics simulation on S a focus function of N-terminal (NTDs) performed. The study reveals that NTD acts as "wedge" and plays crucial regulatory role conformational changes protein. complete RBD structural transition allowed only when neighboring typically prohibits RBD's movements wedge...
Molecular conformation generation aims to generate three-dimensional coordinates of all the atoms in a molecule and is an important task bioinformatics pharmacology. Previous methods usually first predict interatomic distances, gradients distances or local structures (e.g., torsion angles) molecule, then reconstruct its 3D conformation. How directly without above intermediate values not fully explored. In this work, we propose method that predicts atoms: (1) loss function invariant...
The identification of active binding drugs for target proteins (referred to as drug-target interaction prediction) is the key challenge in virtual screening, which plays an essential role drug discovery. Although recent deep learning-based approaches achieve better performance than molecular docking, existing models often neglect topological or spatial intermolecular information, hindering prediction performance. We recognize this problem and propose a novel approach called Intermolecular...
Background Immunohistochemistry (IHC) is a widely used laboratory technique for cancer diagnosis, which selectively binds specific antibodies to target proteins in tissue samples and then makes the bound visible through chemical staining. Deep learning approaches have potential be employed quantifying tumor immune micro-environment (TIME) digitized IHC histological slides. However, it lacks of publicly available datasets explicitly collected in-depth TIME analysis. Method In this paper,...
To determine the epidemiological cut-off values (ECOFFs) of norvancomycin for Staphylococcus aureus, epidermidis, haemolyticus and hominis.We collected 1199 clinical isolates species from five laboratories located in four cities China. MICs inhibitory zone diameters were determined by broth microdilution disc diffusion method, separately. ECOFFs calculated ECOFFinder software following EUCAST principles. Methicillin vancomycin resistance genes (mecA/mecC vanA/vanB/vanC/vanD/vanE) screened...
Abstract This study longitudinally evaluated the immune response in individuals over a year after receiving three doses of an inactivated SARS‐CoV‐2 vaccine, focusing on reactions to Omicron breakthrough infections. From 63 blood samples 37 subjects, results showed that third booster enhanced antibody against Alpha, Beta, and Delta VOCs but was less effective Omicron. Although titres decreased post‐vaccination, SARS‐CoV‐2‐specific T‐cell responses, both CD4 + CD8 , remained stable....
Sphingomyelin (SM) is a reservoir of signaling lipids and forms specific lipid domains in biomembranes together with cholesterol. In this study, atomic force microscopy (AFM) measurement were applied to investigate the interaction SM-binding protein toxin, lysenin, N-palmitoyl-d-erythro-sphingosylphosphorylcholine (palmitoyl sphingomyelin, PSM) bilayer spread over mica substrate, an aqueous buffer solution. Lysenin molecules grafted on silicon nitride tip for AFM by siloxane–thiol–amide...