Artificial intelligence (AI) and deep learning are making groundbreaking strides in protein structure prediction. AlphaFold is remarkable in this arena for its outstanding accuracy in modelling proteins fold based solely on their amino acid sequences...
Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling the determination of biomolecular structures that are challenging to resolve using conventional methods. Interpreting a cryo-EM map requires accurate modeling of the...
Journal of chemical theory and computation
Feb 6, 2025
Graph neural network (GNN) architectures have emerged as promising force field models, exhibiting high accuracy in predicting complex energies and forces based on atomic identities and Cartesian coordinates. To expand the applicability of GNNs, and m...
Journal of chemical information and modeling
Feb 6, 2025
In the realm of drug discovery and design, the accurate prediction of protein-ligand binding affinity is of paramount importance as it underpins the functional interactions within biological systems. This study introduces a novel self-supervised lear...
Protein-ligand structure prediction methods, aiming to predict the three-dimensional complex structure and binding energy of a compound and target protein, are essential in many structure-based drug discovery pipelines, including virtual screening an...
Food research international (Ottawa, Ont.)
Feb 1, 2025
Current detection methods for lipid and protein oxidation using hyperspectral imaging (HSI) in conjunction with machine learning (ML) necessitate the involvement of data scientists and domain experts to adjust the model architecture and tune hyperpar...
Journal of chemical theory and computation
Jan 30, 2025
Despite its importance in understanding biology and computer-aided drug discovery, the accurate prediction of protein ionization states remains a formidable challenge. Physics-based approaches struggle to capture the small, competing contributions in...
In 2021, a year before ChatGPT took the world by storm amid the excitement about generative artificial intelligence (AI), AlphaFold 2 cracked the 50-year-old protein-folding problem, predicting three-dimensional (3D) structures for more than 200 mill...
Journal of chemical information and modeling
Jan 29, 2025
Efficient and accurate drug-target affinity (DTA) prediction can significantly accelerate the drug development process. Recently, deep learning models have been widely applied to DTA prediction and have achieved notable success. However, existing met...
Journal of chemical information and modeling
Jan 28, 2025
Identification of potential drug-target interactions (DTIs) is a crucial step in drug discovery and repurposing. Although deep learning effectively deciphers DTIs, most deep learning-based methods represent drug features from only a single perspectiv...