Metabolites produced in the human gut are known modulators of host immunity. However, large-scale identification of metabolite-host receptor interactions remains a daunting challenge. Here, we employed computational approaches to identify 983 potenti...
Experimental biology and medicine (Maywood, N.J.)
Feb 27, 2021
G protein-coupled receptors (GPCRs) comprise the most important superfamily of protein targets in current ligand discovery and drug development. GPCRs are integral membrane proteins that play key roles in various cellular signaling processes. Therefo...
Substances that can modify the androgen receptor pathway in humans and animals are entering the environment and food chain with the proven ability to disrupt hormonal systems and leading to toxicity and adverse effects on reproduction, brain developm...
Journal of chemical information and modeling
Feb 25, 2021
Graph neural networks are able to solve certain drug discovery tasks such as molecular property prediction and molecule generation. However, these models are considered "black-box" and "hard-to-debug". This study aimed to improve modeling transparen...
BACKGROUND: Differentiating between nontuberculous mycobacterial lung disease (NTM-LD) and pulmonary NTM colonization (NTM-Col) is difficult. Compared with healthy controls, patients with NTM-LD generally present immune tolerance along with increased...
Bioorganic & medicinal chemistry letters
Feb 18, 2021
De novo design of mini-proteins (4-12 kDa) has recently been shown to produce new candidates for protein therapeutics. They are temperature stable molecules that bind to the drug target with high affinity for inhibiting its interactions. The developm...
Journal of molecular graphics & modelling
Feb 9, 2021
Voxel-based 3D convolutional neural networks (CNNs) have been applied to predict protein-ligand binding affinity. However, the memory usage and computation cost of these voxel-based approaches increase cubically with respect to spatial resolution and...
Aptamers can be regarded as efficient substitutes for monoclonal antibodies in many diagnostic and therapeutic applications. Due to the tedious and prohibitive nature of SELEX (systematic evolution of ligands by exponential enrichment), the in silico...
Scoring functions are essential for modern in silico drug discovery. However, the accurate prediction of binding affinity by scoring functions remains a challenging task. The performance of scoring functions is very heterogeneous across different tar...
International journal of molecular sciences
Jan 30, 2021
Computational prediction of Protein-Ligand Interaction (PLI) is an important step in the modern drug discovery pipeline as it mitigates the cost, time, and resources required to screen novel therapeutics. Deep Neural Networks (DNN) have recently show...