Chrombus-XMBD: A Graph Convolution Model Predicting 3D-Genome from Chromatin Features

Research Background and Disciplinary Significance In eukaryotic cells, the three-dimensional (3D) spatial structure of chromatin plays a crucial role in gene expression regulation. Through complex folding, looping, and local spatial reconfiguration of DNA, different genetic elements (such as promoters and enhancers) are brought into spatial proximi...

TopoQA: A Topological Deep Learning-Based Approach for Protein Complex Structure Interface Quality Assessment

Academic Background The elucidation of protein complex 3D structures is a central topic in modern structural biology, molecular mechanism studies, drug design, and even artificial protein design. The function of a protein is often determined by its structure, and many biological processes involve complex interactions between proteins. Although trad...

DockEM: An Enhanced Method for Atomic-Scale Protein–Ligand Docking Refinement Leveraging Low-to-Medium Resolution Cryo-EM Density Maps

Academic Background and Research Motivation In recent years, protein–ligand docking has rapidly developed as a core technology for virtual drug screening and structure-based drug discovery. Despite improvements in drug discovery efficiency through large-scale high-throughput screening technologies, new drug development still faces high costs, long ...

Regularly Updated Benchmark Sets for Statistically Correct Evaluations of AlphaFold Applications

Academic Background: Crossing into a New Era of Protein Structure Prediction Protein structure determination has long stood as one of the central challenges in molecular biology and life sciences. Traditional experimental methods such as X-ray crystallography, nuclear magnetic resonance (NMR), and cryo-electron microscopy have provided a solid foun...

In Situ Architecture of the Human Prohibitin Complex

Academic Background Mitochondria are the energy factories of cells, and the integrity of the mitochondrial inner membrane (MIM) is crucial for cellular function. Prohibitin (PHB) is a highly conserved protein family, consisting of two subtypes, PHB1 and PHB2, which play important roles in various cellular processes, including mitochondrial stress s...