Cold Spring Harbor perspectives in biology
Sep 3, 2024
From over to , the recent decade of exponential advances in artificial intelligence (AI) has been altering life. In parallel, advances in computational biology are beginning to decode the language of life: leaped forward in protein structure predi...
BACKGROUND: Recently, the process of evolution information and the deep learning network has promoted the improvement of protein contact prediction methods. Nevertheless, still remain some bottleneck: (1) One of the bottlenecks is the prediction of o...
International journal of molecular sciences
Aug 27, 2024
Predicting protein-ligand binding sites is an integral part of structural biology and drug design. A comprehensive understanding of these binding sites is essential for advancing drug innovation, elucidating mechanisms of biological function, and exp...
Annotating active sites in enzymes is crucial for advancing multiple fields including drug discovery, disease research, enzyme engineering, and synthetic biology. Despite the development of numerous automated annotation algorithms, a significant trad...
Chemical structures of protein surfaces govern intermolecular interaction, and protein functions include specific molecular recognition, transport, self-assembly, etc. Therefore, the relationship between the chemical structure and protein functions p...
Ligand binding site prediction is a crucial initial step in structure-based drug discovery. Although several methods have been proposed previously, including those using geometry based and machine learning techniques, their accuracy is considered to ...
BACKGROUND: Proteins play a pivotal role in the diverse array of biological processes, making the precise prediction of protein-protein interaction (PPI) sites critical to numerous disciplines including biology, medicine and pharmacy. While deep lear...
High-throughput proteomics approaches have revolutionised the identification of RNA-binding proteins (RBPome) and RNA-binding sequences (RBDome) across organisms. Yet, the extent of noise, including false positives, associated with these methodologie...
Journal of the American Society for Mass Spectrometry
Jul 29, 2024
In computational proteomics, machine learning (ML) has emerged as a vital tool for enhancing data analysis. Despite significant advancements, the diversity of ML model architectures and the complexity of proteomics data present substantial challenges...
Membrane proteins are considered the major source of drug targets and are indispensable for drug design and disease prevention. However, traditional biomechanical experiments are costly and time-consuming; thus, many computational methods for predict...