Journal of chemical information and modeling
Feb 22, 2024
Developing new drugs is too expensive and time -consuming. Accurately predicting the interaction between drugs and targets will likely change how the drug is discovered. Machine learning-based protein-ligand interaction prediction has demonstrated si...
Journal of chemical information and modeling
Feb 17, 2024
Predicting the binding affinity of protein-ligand complexes is crucial for computer-aided drug discovery (CADD) and the identification of potential drug candidates. The deep learning-based scoring functions have emerged as promising predictors of bin...
When designing a machine learning-based scoring function, we access a limited number of protein-ligand complexes with experimentally determined binding affinity values, representing only a fraction of all possible protein-ligand complexes. Consequent...
Current opinion in structural biology
Feb 13, 2024
Allosteric regulation is a fundamental biological mechanism that can control critical cellular processes via allosteric modulator binding to protein distal functional sites. The advantages of allosteric modulators over orthosteric ones have sparked t...
The rank ordering of ligands remains one of the most attractive challenges in drug discovery. While physics-based in silico binding affinity methods dominate the field, they still have problems, which largely revolve around forcefield accuracy and sa...
Cell-cell communication is essential to many key biological processes. Intercellular communication is generally mediated by ligand-receptor interactions (LRIs). Thus, building a comprehensive and high-quality LRI resource can significantly improve in...
Phosphoinositide 3-kinase alpha (PI3Kα) is one of the most frequently dysregulated kinases known for their pivotal role in many oncogenic diseases. While the side effects linked to existing drugs against PI3Kα-induced cancers provide an avenue for fu...
Predicting protein-ligand binding affinity presents a viable solution for accelerating the discovery of new lead compounds. The recent widespread application of machine learning approaches, especially graph neural networks, has brought new advancemen...
Cyclooxygenase-2 (COX-2) inhibitors are nonsteroidal anti-inflammatory drugs that treat inflammation, pain and fever. This study determined the interaction mechanisms of COX-2 inhibitors and the molecular properties needed to design new drug candidat...
Molecular recognition is fundamental in biology, underpinning intricate processes through specific protein-ligand interactions. This understanding is pivotal in drug discovery, yet traditional experimental methods face limitations in exploring the va...