A5062764236- Protein Structure and Dynamics
- Computational Drug Discovery Methods
- RNA and protein synthesis mechanisms
- Enzyme Structure and Function
- Bacteriophages and microbial interactions
- Bacterial Genetics and Biotechnology
- RNA Research and Splicing
- Groundwater flow and contamination studies
- Heavy metals in environment
- Chemical Synthesis and Analysis
- MicroRNA in disease regulation
- Heavy Metal Exposure and Toxicity
- Tryptophan and brain disorders
- Hydrology and Watershed Management Studies
- Viral gastroenteritis research and epidemiology
- SARS-CoV-2 and COVID-19 Research
- Groundwater and Isotope Geochemistry
- Machine Learning in Materials Science
- Machine Learning in Bioinformatics
- COVID-19 epidemiological studies
- Advanced Proteomics Techniques and Applications
- Medicinal Plants and Neuroprotection
- Immune Response and Inflammation
- Autophagy in Disease and Therapy
- vaccines and immunoinformatics approaches
Zhengzhou University
2024-2025
Yale University
2025
Novo Nordisk Foundation
2022-2024
University of Copenhagen
2022-2024
China Medical University
2019-2024
Foundation Center
2024
Institute of Biophysics
2018-2023
Chinese Academy of Sciences
2023
Huazhong University of Science and Technology
2016-2023
Jilin University
2023
Protein-protein and protein-DNA/RNA interactions play a fundamental role in variety of biological processes. Determining the complex structures these is valuable, which molecular docking has played an important role. To automatically make use binding information from PDB docking, here we have presented HDOCK, novel web server our hybrid algorithm template-based modeling free cases with misleading templates can be rescued by protocol. The supports protein-protein accepts both sequence...
The outbreak of a novel coronavirus, which was later formally named the severe acute respiratory coronavirus 2 (SARS-CoV-2), has caused worldwide public health crisis. Previous studies showed that SARS-CoV-2 is highly homologous to SARS-CoV and infects humans through binding spike protein ACE2. Here, we have systematically studied molecular mechanisms human infection with by protein-protein docking MD simulations. It found binds ACE2 higher affinity than SARS-CoV, may partly explain much...
Abstract Extracellular cytokines are enriched in the tumor microenvironment and regulate various important properties of cancers, including autophagy. However, precise molecular mechanisms underlying link between autophagy extracellular remain to be elucidated. In present study, we demonstrate that IL-6 activates through IL-6/JAK2/BECN1 pathway promotes chemotherapy resistance colorectal cancer (CRC). Mechanistically, triggers interaction JAK2 BECN1, where phosphorylates BECN1 at Y333. We...
Protein-protein docking is an important computational tool for predicting protein-protein interactions. With the rapid development of proteomics projects, more and experimental binding information ranging from mutagenesis data to three-dimensional structures protein complexes are becoming available. Therefore, how appropriately incorporate biological into traditional ab initio has been issue challenge in field docking. To address these challenges, we have developed a Hybrid DOCKing protocol...
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....
Abstract Protein–protein interactions play a fundamental role in all cellular processes. Therefore, determining the structure of protein–protein complexes is crucial to understand their molecular mechanisms and develop drugs targeting interactions. Recently, deep learning has led breakthrough intra-protein contact prediction, achieving an unusual high accuracy recent Critical Assessment protein Structure Prediction (CASP) prediction challenges. However, due limited number known homologous...
Conformation generation of protein-bound peptides is critical for the determination protein–peptide complex structures. Despite significant progress in conformer small molecules, few methods have been developed modeling peptide conformations. Here, we a fast de novo algorithm, referred to as MODPEP, conformational sampling peptides. Given sequence, MODPEP builds 3D structure from scratch by assembling amino acids or helix fragments based on constructed rotamer and libraries. The algorithm...
Given the importance of peptide-mediated protein interactions in cellular processes, protein–peptide docking has received increasing attention. Here, we have developed a Hierarchical flexible Peptide Docking approach through fast generation and ensemble peptide conformations, which is referred to as HPepDock. Tested on LEADS-PEP benchmark data set 53 diverse complexes with peptides 3–12 residues, HPepDock performed significantly better than 11 protocols five small-molecule programs (DOCK,...
A major subclass of protein-protein interactions is formed by homo-oligomers with certain symmetry. Therefore, computational modeling the symmetric protein complexes important for understanding molecular mechanism related biological processes. Although several docking algorithms have been developed Cn symmetry, few servers proposed Dn Here, we present HSYMDOCK, a web server our hierarchical algorithm that supports both and The HSYMDOCK was extensively evaluated on three benchmarks complexes,...
Abstract Background Protein-protein docking is a valuable computational approach for investigating protein-protein interactions. Shape complementarity the most basic component of scoring function and plays an important role in docking. Despite significant progresses, shape representation remains open question development algorithms, especially grid-based approaches. Results We have proposed new pairwise shape-based (LSC) which adopts exponential form to take into account long-range...
Protein-protein interactions play an important role in many biological processes. However, although structure prediction for monomer proteins has achieved great progress with the advent of advanced deep learning algorithms like AlphaFold, protein-protein complexes remains open question. Taking advantage Transformer model ESM-MSA, we have developed a learning-based model, named DeepHomo2.0, to predict homodimeric by leveraging direct-coupling analysis (DCA) and features sequences monomers....
Abstract Membrane proteins are encoded by approximately a quarter of human genes. Inter-chain residue-residue contact information is important for structure prediction membrane protein complexes and valuable understanding their molecular mechanism. Although many deep learning methods have been proposed to predict the intra-protein contacts or helix-helix interactions in proteins, it still challenging accurately inter-chain due limited number transmembrane proteins. Addressing challenge, here...
In recent years, industrial and agricultural advancements in Henan Province have increased heavy metal contamination rice, raising public concerns. The aim of this study was to investigate the levels five metals, cadmium (Cd), chromium (Cr), lead (Pb), mercury (Hg), inorganic arsenic (As), rice from assess potential health risks. A total 6,632 samples were collected 18 regions between 2020 2022. analyzed for Cd, Cr, Pb, Hg, As using inductively coupled plasma mass spectrometry (ICP-MS)....
Summary Zorya is a recently identified and widely distributed bacterial immune system, which protects against phage invasion. It consists of predicted membrane-embedded complex (ZorAB) soluble components that differ among subtypes, notably ZorC ZorD, in type I systems. Here, we reveal the molecular basis defense system using cryo-electron microscopy, mutagenesis, fluorescence proteomics, functional studies. We demonstrate ZorAB shares stoichiometry other 5:2 inner membrane ion-driven rotary...
Abstract Since December, 2019, an outbreak of pneumonia caused by the new coronavirus (2019-nCoV) has hit city Wuhan in Hubei Province. With continuous development epidemic, it become a national public health crisis and calls for urgent antiviral treatments or vaccines. The spike protein on envelope is critical host cell infection virus vitality. Previous studies showed that 2019-nCoV highly homologous to human SARS-CoV attaches cells though binding receptor domain (RBD)...
Highly selective microstrip bandpass filters in Ka-band are developed by suitably inserting the attenuation poles an edge-coupled structure. The at high and low passband edges introduced adding a capacitively coupled gap tapped open stubs conventional filter. In this study, improved with center frequencies 28 GHz 38 fabricated on Teflon Al2O3 substrates. Both have better selectivity occupy same area when compared
Protein-protein docking plays an important role in the computational prediction of complex structure between two proteins. For years, a variety algorithms have been developed, as witnessed by critical assessment interactions (CAPRI) experiments. However, despite their successes, many often require series manual operations like modeling structures from sequences, incorporating biological information, and selecting final models. The difficulties these steps significantly limited applications...