MOTIVATION: To provide high quality, computationally tractable annotation of binding sites for biologically relevant (cognate) ligands in UniProtKB using the chemical ontology ChEBI (Chemical Entities of Biological Interest), to better support effort...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
Novel design of proteins to target receptors for treatment or tissue augmentation has come to the fore owing to advancements in computing power, modeling frameworks, and translational successes. Shorter proteins, or peptides, can offer combinatorial ...
Protein science : a publication of the Protein Society
Dec 1, 2022
Knowledge of protein-ligand interactions is beneficial for biological process analysis and drug design. Given the complexity of the interactions and the inadequacy of experimental data, accurate ligand binding residue and pocket prediction remains ch...
MOTIVATION: The capability to predict the potential drug binding affinity against a protein target has always been a fundamental challenge in silico drug discovery. The traditional experiments in vitro and in vivo are costly and time-consuming which ...
G protein-coupled receptors (GPCRs) are valuable therapeutic targets for many diseases. A central question of GPCR drug discovery is to understand what determines the agonism or antagonism of ligands that bind them. Ligands exert their action via the...
Nuclear receptors (NRs) are ligand-activated transcription factors, which constitute one of the most important targets for drug discovery. Current computational strategies mainly focus on a single target, and the transfer of learned knowledge among N...
MOTIVATION: Machine-learning-based prediction of compound-protein interactions (CPIs) is important for drug design, screening and repurposing. Despite numerous recent publication with increasing methodological sophistication claiming consistent impro...
We construct a protein-protein interaction (PPI) targeted drug-likeness dataset and propose a deep molecular generative framework to generate novel drug-likeness molecules from the features of the seed compounds. This framework gains inspiration from...
Recent advances in protein structural modelling have enabled the accurate prediction of the holo 3D structures of almost any protein, however protein function is intrinsically linked to the interactions it makes. While a number of computational appro...
Proteins are essential macromolecules for the maintenance of living systems. Many of them perform their function by interacting with other molecules in regions called binding sites. The identification and characterization of these regions are of fund...
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