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...
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...
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...
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, ...
International journal of molecular sciences
Oct 16, 2022
Peptide detectability is defined as the probability of identifying a peptide from a mixture of standard samples, which is a key step in protein identification and analysis. Exploring effective methods for predicting peptide detectability is helpful f...
A fundamental question in protein science is where allosteric hotspots - residues critical for allosteric signaling - are located, and what properties differentiate them. We carried out deep mutational scanning (DMS) of four homologous bacterial allo...
Imaging is commonly used as a characterization method in the pharmaceuticals industry, including for quantifying subvisible particles in solid and liquid formulations. Extracting information beyond particle size, such as classifying morphological sub...