Peptides are an emerging modality for developing therapeutics that can either agonize or antagonize cellular pathways associated with disease, yet peptides often suffer from poor chemical and physical stability, which limits their potential. However,...
Biomolecular dynamics simulation is a fundamental technology for life sciences research, and its usefulness depends on its accuracy and efficiency. Classical molecular dynamics simulation is fast but lacks chemical accuracy. Quantum chemistry methods...
MOTIVATION: Due to the breakthrough in protein structure prediction by AlphaFold, the scientific community has access to 200 million predicted protein structures with near-atomic accuracy from the AlphaFold protein structure DataBase (AFDB), covering...
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...
Methods in molecular biology (Clifton, N.J.)
39576578
Protein structure prediction is fundamental to molecular biology and has numerous applications in areas such as drug discovery and protein engineering. Machine learning techniques have greatly advanced protein 3D modeling in recent years, particularl...
Proceedings of the National Academy of Sciences of the United States of America
39951500
Understanding the dynamic evolution of protein structures is crucial for uncovering their biological functions. Yet, real-time prediction of these dynamic structures remains a significant challenge. Two-dimensional infrared (2DIR) spectroscopy is a p...
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...
Journal of chemical theory and computation
40105797
A major challenge for many rare-event sampling strategies is the identification of progress coordinates that capture the slowest relevant motions. Machine-learning methods that can identify progress coordinates in an unsupervised manner have therefor...
Membrane protein folding in the viscous microenvironment of a lipid bilayer is an inherently slow process that challenges experiments and computational efforts alike. The folding kinetics is moreover associated with topological modulations of the bio...
Models of protein structures enable molecular understanding of biological processes. Current protein structure prediction tools lie at the interface of biology, chemistry and computer science. Millions of protein structure models have been generated ...