Structure-based machine learning algorithms have been utilized to predict the properties of protein-protein interaction (PPI) complexes, such as binding affinity, which is critical for understanding biological mechanisms and disease treatments. While...
Interdisciplinary sciences, computational life sciences
Nov 6, 2024
Circular RNA (circRNA) has the capacity to bind with RNA binding protein (RBP), thereby exerting a substantial impact on diseases. Predicting binding sites aids in comprehending the interaction mechanism, thereby offering insights for disease treatme...
IEEE transactions on pattern analysis and machine intelligence
Nov 6, 2024
Inductive bias in machine learning (ML) is the set of assumptions describing how a model makes predictions. Different ML-based methods for protein-ligand binding affinity (PLA) prediction have different inductive biases, leading to different levels o...
The identification of protein binding residues is essential for understanding their functions in vivo. However, it remains a computational challenge to accurately identify binding sites due to the lack of known residue binding patterns. Local residue...
European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences
Oct 28, 2024
Plasma protein binding (PPB) is closely related to pharmacokinetics, pharmacodynamics and drug toxicity. Existing models for predicting PPB often suffer from low prediction accuracy and poor interpretability, especially for high PPB compounds, and ar...
International journal of biological macromolecules
Oct 28, 2024
Protein-protein/peptide interactions play crucial roles in various biological processes. Exploring their interactions attracts wide attention. However, accurately predicting their binding sites remains a challenging task. Here, we develop an effectiv...
The high binding affinity of antibodies toward their cognate targets is key to eliciting effective immune responses, as well as to the use of antibodies as research and therapeutic tools. Here, we propose ANTIPASTI, a convolutional neural network mod...
HLA-DRB1*04:01 is associated with numerous diseases, including sclerosis, arthritis, diabetes, and COVID-19, emphasizing the need to scan for binders in the antigens to develop immunotherapies and vaccines. Current prediction methods are often limite...
IEEE/ACM transactions on computational biology and bioinformatics
Oct 9, 2024
Accurate prediction of Drug-Target binding Affinity (DTA) is a daunting yet pivotal task in the sphere of drug discovery. Over the years, a plethora of deep learning-based DTA models have emerged, rendering promising results in predicting the binding...
The G protein-coupled receptor 40 (GPR40) is known to exert a significant influence on neurogenesis and neurodevelopment within the central nervous system of both humans and rodents. Research findings indicate that the activation of GPR40 by an agoni...