7 accepted papers
Deep learning models have driven significant progress in predicting protein function and interactions at the protein level. While these advancements have been invaluable for many biological applications such as enzyme engineering and function annotation, a more detailed perspective is essential for…
In-silico prediction of protein mutant stability, measured by the difference in Gibbs free energy change ($\Delta \Delta G$), is fundamental for protein engineering. Current sequence-to-label methods typically employ two-stage pipelines: (i) encoding mutant sequences using neural networks (e.g., tra…
Protein language models (PLMs) have shown remarkable capabilities in various protein function prediction tasks. However, while protein function is intricately tied to structure, most existing PLMs do not incorporate protein structure information. To address this issue, we introduce ProSST, a Transfo…
Enzymes, with their specific catalyzed reactions, are necessary for all aspects of life, enabling diverse biological processes and adaptations. Predicting enzyme functions is essential for understanding biological pathways, guiding drug development, enhancing bioproduct yields, and facilitating evol…
The dynamic nature of proteins is crucial for determining their biological functions and properties, for which Monte Carlo (MC) and molecular dynamics (MD) simulations stand as predominant tools to study such phenomena. By utilizing empirically derived force fields, MC or MD simulations explore the…
Proteins play a critical role in carrying out biological functions, and their 3D structures are essential in determining their functions. Accurately predicting the conformation of protein side-chains given their backbones is important for applications in protein structure prediction, design and pro…
Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standing challenge in the field of bioengineering. Existing approaches generate both protein sequence and structure using eith…