IEEE journal of biomedical and health informatics
Jul 2, 2024
Binding affinity prediction of three-dimensional (3D) protein-ligand complexes is critical for drug repositioning and virtual drug screening. Existing approaches usually transform a 3D protein-ligand complex to a two-dimensional (2D) graph, and then ...
The clustering of death receptors (DRs) at the membrane leads to apoptosis. With the goal of treating tumours, multivalent molecular tools that initiate this mechanism have been developed. However, DRs are also ubiquitously expressed in healthy tissu...
Journal of chemical information and modeling
Jul 1, 2024
Scaffold-hopped (SH) compounds are bioactive compounds structurally different from known active compounds. Identifying SH compounds in the ligand-based approaches has been a central issue in medicinal chemistry, and various molecular representations ...
AlphaFold2 (AF2) models have had wide impact but mixed success in retrospective ligand recognition. We prospectively docked large libraries against unrefined AF2 models of the σ and serotonin 2A (5-HT2A) receptors, testing hundreds of new molecules a...
Classical scoring functions may exhibit low accuracy in determining ligand binding affinity for proteins. The availability of both protein-ligand structures and affinity data make it possible to develop machine-learning models focused on specific pro...
Virtual screening (VS) is one of the well-established approaches in drug discovery which speeds up the search for a bioactive molecule and, reduces costs and efforts associated with experiments. VS helps to narrow down the search space of chemical sp...
Journal of chemical information and modeling
Jun 7, 2024
We present a novel and interpretable approach for assessing small-molecule binding using context explanation networks. Given the specific structure of a protein/ligand complex, our CENsible scoring function uses a deep convolutional neural network to...
Journal of chemical information and modeling
Jun 6, 2024
Determining the viability of a new drug molecule is a time- and resource-intensive task that makes computer-aided assessments a vital approach to rapid drug discovery. Here we develop a machine learning algorithm, iMiner, that generates novel inhibit...
Structure-based virtual screening utilizes molecular docking to explore and analyze ligand-macromolecule interactions, crucial for identifying and developing potential drug candidates. Although there is availability of several widely used docking pro...
Journal of bioinformatics and computational biology
May 27, 2024
Biomolecular interaction recognition between ligands and proteins is an essential task, which largely enhances the safety and efficacy in drug discovery and development stage. Studying the interaction between proteins and ligands can improve the unde...