A5071710594- Protein Structure and Dynamics
- Computational Drug Discovery Methods
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Enzyme Structure and Function
- RNA modifications and cancer
- DNA and Nucleic Acid Chemistry
- HIV/AIDS drug development and treatment
- Machine Learning in Bioinformatics
- Machine Learning in Materials Science
- vaccines and immunoinformatics approaches
- HIV Research and Treatment
- Monoclonal and Polyclonal Antibodies Research
- RNA Research and Splicing
- Peptidase Inhibition and Analysis
- Glycosylation and Glycoproteins Research
- Biochemical and Molecular Research
- Chemical Synthesis and Analysis
- Drug Transport and Resistance Mechanisms
- Hepatitis C virus research
- Ubiquitin and proteasome pathways
- Nicotinic Acetylcholine Receptors Study
- Epigenetics and DNA Methylation
- Lung Cancer Treatments and Mutations
- Lung Cancer Research Studies
Jiangsu University of Technology
2016-2025
Sungkyunkwan University
2025
Inner Mongolia University for Nationalities
2025
Jiangxi Normal University
2024
Donghua University
2024
Jiangsu University
2023
Soochow University
2023
Ocean University of China
2023
Qingdao National Laboratory for Marine Science and Technology
2020
European Bioinformatics Institute
2020
Motivation: The coronavirus disease 2019 (COVID-19) caused by a new type of has been emerging from China and led to thousands death globally since December 2019. Despite many groups have engaged in studying the newly emerged virus searching for treatment COVID-19, understanding COVID-19 target-ligand interactions represents key chal-lenge. Herein, we introduce Docking Server, web server that predicts binding modes between targets ligands including small molecules, peptides anti-bodies....
Abstract With the emergence of multidrug-resistant bacteria, antimicrobial peptides (AMPs) offer promising options for replacing traditional antibiotics to treat bacterial infections, but discovering and designing AMPs using methods is a time-consuming costly process. Deep learning has been applied de novo design address AMP classification with high efficiency. In this study, several natural language processing models were combined identify AMPs, i.e. sequence generative adversarial nets,...
Abstract We present the results for CAPRI Round 54, 5th joint CASP‐CAPRI protein assembly prediction challenge. The offered 37 targets, including 14 homodimers, 3 homo‐trimers, 13 heterodimers antibody–antigen complexes, and 7 large assemblies. On average ~70 CASP predictor groups, more than 20 automatics servers, submitted models each target. A total of 21 941 by these groups 15 scorer were evaluated using model quality measures DockQ score consolidating measures. performance was quantified...
Genome-wide association study (GWAS) is nowadays widely used to identify genes involved in human complex disease. The standard GWAS analysis examines SNPs/genes independently and identifies only a number of the most significant SNPs. It ignores combined effect weaker SNPs/genes, which leads difficulties explore biological function mechanism from systems point view. Although gene set enrichment (GSEA) has been introduced overcome these limitations by identifying correlation between...
We present the results for CAPRI Round 46, third joint CASP-CAPRI protein assembly prediction challenge. The comprised a total of 20 targets including 14 homo-oligomers and 6 heterocomplexes. Eight homo-oligomer one heterodimer proteins that could be readily modeled using templates from Protein Data Bank, often available full assembly. remaining 11 5 homodimers, 3 heterodimers, two higher-order assemblies. These were more difficult to model, as their mainly involved "ab-initio" docking...
Abstract We present the results for CAPRI Round 50, fourth joint CASP‐CAPRI protein assembly prediction challenge. The comprised a total of twelve targets, including six dimers, three trimers, and higher‐order oligomers. Four these were easy which good structural templates available either full assembly, or main interfaces (of oligomers). Eight difficult targets only distantly related found individual subunits. Twenty‐five groups eight automatic servers submitted ~1250 models per target....
Cancer is ranked as one of the top killers in all human diseases and continues to have a devastating effect on population around globe. Current research efforts are aiming accelerate our understanding molecular basis cancer develop effective means for diagnostics, treatment prognosis. An altered pattern epigenetic modifications, most importantly DNA methylation events, plays critical role tumorigenesis through regulating oncogene activation, tumor suppressor gene silencing chromosomal...
Specific interactions between scaffold protein SH3 and multiple ankyrin repeat domains 3 (Shank3) synapse-associated 90/postsynaptic density-95⁻associated (SAPAP) are essential for excitatory synapse development plasticity. In a bunch of human neurological diseases, mutations on Shank3 or SAPAP detected. To investigate the dynamical thermodynamic properties specific binding N-terminal extended PDZ (Post-synaptic density-95/Discs large/Zonaoccludens-1) domain (N-PDZ) motif (E-PBM) SAPAP,...
The accurate predicting of physical properties and bioactivity drug molecules in deep learning depends on how are represented. Many types molecular descriptors have been developed for quantitative structure-activity/property relationships structure-activity (QSPR). However, each descriptor is optimized a specific application with encoding preference. Considering that standalone featurization methods may only cover parts information the chemical molecules, we proposed to build conjoint...
Accurately predicting molecular properties is a challenging but essential task in drug discovery. Recently, many mono-modal deep learning methods have been successfully applied to property prediction. However, inherently limited as it relies solely on single modality of representation, which restricts comprehensive understanding molecules. To overcome the limitations, we propose multimodal fused (MMFDL) model leverage information from different representations. Specifically, construct...
Genome-wide association study (GWAS) is widely utilized to identify genes involved in human complex disease or some other trait. One key challenge for GWAS data interpretation causal SNPs and provide profound evidence on how they affect the Currently, researches are focusing identification of candidate variants from most significant GWAS, while there lack support biological mechanisms as represented by pathways. Although pathway-based analysis (PBA) has been designed disease-related pathways...
DNA methyltransferases (DNMTs), responsible for the regulation of methylation, have been regarded as promising drug targets cancer therapy. However, high structural conservation catalytic domains DNMTs poses a big challenge to design selective inhibitors specific DNMT isoform. In this study, molecular dynamics (MD) simulations, end-point free energy calculations and umbrella sampling (US) simulations were performed reveal basis binding selectivity three representative towards DNMT1 DNMT3A,...
The interaction between human complement receptor type 2 (CR2) and antigen-bound C3d can bridge the innate adaptive immune systems. recently determined structure of CR2(SCR1-2):C3d complex has revealed expected binding interface CR2-C3d. In this article, wild (WT) three mutants new are studied by molecular dynamics (MD) simulations. differently decreased structural stabilities relative to WT shown be consistent with experimental data, which explained different hydrogen bond patterns at...
Abstract Androgen receptor (AR) is a ligand-activated transcription factor that plays pivotal role in the development and progression of many severe diseases such as prostate cancer, muscle atrophy, osteoporosis. Binding ligands to AR triggers conformational changes may affect recruitment coactivators downstream response signaling pathway. Therefore, have great potential treat these diseases. In this study, we searched for novel by performing docking-based virtual screening (VS) on basis...
Protein–protein docking technology is an effective approach to study the molecular mechanism of essential biological processes mediated by complex protein–protein interactions. The fast Fourier transform (FFT) correlation makes a good balance between exhaustive global sampling and computational efficiency for docking. However, it difficult integrate precise knowledge-based scoring function site constraint information into FFT-based approach. New strategies with capability combining both are...
Predicting the impact of mutations on protein-ligand binding affinity is crucial in drug discovery, particularly addressing resistance and repurposing existing drugs. Current structure-based methods, including deep learning physics-based computational techniques, are constrained by their dependence known complex structures. The lack structural data for mutated proteins, coupled with potential to alter protein conformational states, poses challenges reliable predictions. To address challenge,...
B-cell epitope prediction is crucial for advancing immunology, particularly in vaccine development and antibody-based therapies. Traditional experimental techniques are hindered by high costs, time consumption, limited scalability, making them unsuitable large-scale applications. Computational methods provide a promising alternative, enabling high-throughput screening accurate predictions. However, existing computational approaches often struggle to capture the complexity of protein...
Rubus corchorifolius, a medicinal plant of the Rosaceae family, is known for its diverse bioactive compounds. This study employs widely targeted metabolomics to investigate metabolic profiles leaf, stem, and flower tissue from R. corchorifolius. Using ultra-performance liquid chromatography coupled with tandem mass spectrometry, we identified 1,946 metabolites across three types. Multivariate statistical analyses revealed distinct signatures each tissue, flowers showing most distinctive...
COL17A1 is predominantly expressed in skin epithelial cells and primarily localized within hemidesmosomes. It plays an essential role epidermal–dermal attachment. Consequently, a recombinant human-like protein (rhCOL17) with low molecular weight high biocompatibility presents promising competitive biomaterial. The aim of this study to gain more insight into the biological functions underlying mechanisms rhCOL17, which consists amino acid residues Gly659-Leu720. Using combination surface...
Frequent outbreaks of highly pathogenic avian influenza and the increasing data available for comparative analysis require a central database specialized in viruses (IVs). We have established Influenza Virus Database (IVDB) to integrate information create an platform genetic, genomic, phylogenetic studies virus. IVDB hosts complete genome sequences A virus generated by Beijing Institute Genomics (BIG) curates all other published IV after expert annotation. Our Q-Filter system classifies...
TAL (transcriptional activator-like) effectors (TALEs) are DNA-binding proteins, containing a modular central domain that recognizes specific DNA sequences. Recently, the crystallographic studies of TALEs revealed structure DNA-recognition domain. In this article, molecular dynamics (MD) simulations employed to study two crystal structures an 11.5-repeat TALE, in presence and absence DNA, respectively. The simulated results indicate binding RVDs (repeat-variable diresidues) with leads...