Proteins are molecular machinery that participate in virtually all essential biological functions within the cell, which are tightly related to their 3D structure. The importance of understanding protein structure-function relationship is highlighted...
Accurately predicting protein-ligand binding affinities is crucial for determining molecular properties and understanding their physical effects. Neural networks and transformers are the predominant methods for sequence modeling, and both have been s...
This paper addresses the crucial task of identifying DNA/RNA binding sites, which has implications in drug/vaccine design, protein engineering, and cancer research. Existing methods utilize complex neural network structures, diverse input types, and ...
Journal of biomolecular structure & dynamics
Oct 12, 2023
The identification of potential epigenetic targets for a known bioactive compound is essential and promising as more and more epigenetic drugs are used in cancer clinical treatment and the availability of chemogenomic data related to epigenetics incr...
Protein-ligand interaction plays a crucial role in drug discovery, facilitating efficient drug development and enabling drug repurposing. Several computational algorithms, such as Graph Neural Networks and Convolutional Neural Networks, have been pro...
IEEE/ACM transactions on computational biology and bioinformatics
Oct 9, 2023
Circular RNA (CircRNA) is widely expressed and has physiological and pathological significance, regulating post-transcriptional processes via its protein-binding activity. However, whereas much work has been done on linear RNA and RNA binding protein...
IEEE/ACM transactions on computational biology and bioinformatics
Oct 9, 2023
Protein binding site prediction is an important prerequisite task of drug discovery and design. While binding sites are very small, irregular and varied in shape, making the prediction very challenging. Standard 3D U-Net has been adopted to predict b...
IEEE/ACM transactions on computational biology and bioinformatics
Oct 9, 2023
RNA-binding proteins are important for the process of cell life activities. High-throughput technique experimental method to discover RNA-protein binding sites is time-consuming and expensive. Deep learning is an effective theory for predicting RNA-p...
Ligand docking is one of the core technologies in structure-based virtual screening for drug discovery. However, conventional docking tools and existing deep learning tools may suffer from limited performance in terms of speed, pose quality and bindi...
International journal of biological macromolecules
Aug 24, 2023
Proteins play a crucial role in many biological processes, where their interaction with other proteins are integral. Abnormal protein-protein interactions (PPIs) have been linked to various diseases including cancer, and thus targeting PPIs holds pro...
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