Molecular diversity
Nov 11, 2022
Kinase plays a significant role in various disease signaling pathways. Due to the highly conserved sequence of kinase family members, understanding the selectivity profile of kinase inhibitors remains a priority for drug discovery. Previous methods f...
International journal of molecular sciences
Nov 11, 2022
Accurately predicting ligand binding affinity in a virtual screening campaign is still challenging. Here, we developed hybrid neural network (HNN) machine deep learning methods, HNN-denovo and HNN-affinity, by combining the 3D-CNN (convolutional neur...
Current opinion in structural biology
Nov 10, 2022
Significant advances have been achieved in protein structure prediction, especially with the recent development of the AlphaFold2 and the RoseTTAFold systems. This article reviews the progress in deep learning-based protein structure prediction metho...
Interdisciplinary sciences, computational life sciences
Nov 8, 2022
PURPOSE: The determination of which amino acid in a protein interacts with other proteins is important in understanding the functional mechanism of that protein. Although there are experimental methods to detect protein-protein interaction sites (PPI...
BMC bioinformatics
Nov 8, 2022
Pre-trained natural language processing models on a large natural language corpus can naturally transfer learned knowledge to protein domains by fine-tuning specific in-domain tasks. However, few studies focused on enriching such protein language mod...
Journal of chemical information and modeling
Nov 7, 2022
The analysis and comparison of protein-binding sites aid various applications in the drug discovery process, e.g., hit finding, drug repurposing, and polypharmacology. Classification of binding sites has been a hot topic for the past 30 years, and ma...
Scientific reports
Oct 31, 2022
Identifying the binding between the target proteins and molecules is essential in drug discovery. The multi-task learning method has been introduced to facilitate knowledge sharing among tasks when the amount of information for each task is small. Ho...
Journal of visualized experiments : JoVE
Oct 28, 2022
The retinal pigment epithelium (RPE) and retina are functionally and structurally connected tissues that work together to regulate light perception and vision. Proteins on the RPE apical surface are tightly associated with proteins on the photorecept...
Journal of chemical information and modeling
Oct 21, 2022
In structure-based virtual screening (SBVS), it is critical that scoring functions capture protein-ligand atomic interactions. By focusing on the local domains of ligand binding pockets, a standardized pocket Pfam-based clustering (Pfam-cluster) appr...
Nature communications
Oct 18, 2022
Nuclear Magnetic Resonance (NMR) spectroscopy is a major technique in structural biology with over 11,800 protein structures deposited in the Protein Data Bank. NMR can elucidate structures and dynamics of small and medium size proteins in solution, ...