3 papers
physics.chem-ph2026
DeltaDiff: Training-Free, Physics-Guided Machine Learning for Predicting Mutant Protein Structures
Yajie Cai, Yanbin Wang, Ming Chen
Determining mutant protein structures is critical for understanding the mechanistic roles of mutations in biochemical processes. However, experimental characterization and conventi…
physics.bio-ph2025
ProTDyn: a foundation Protein language model for Thermodynamics and Dynamics generation
Yikai Liu, Haoyang Zheng, Lining Mao +3
Molecular dynamics (MD) simulation has long been the principal computational tool for exploring protein conformational landscapes and dynamics, but its application is limited by hi…
physics.chem-ph2025
Constructing Generalized Sample Transition Probabilities with Biased Simulations
Yanbin Wang, Jakub Rydzewski, Ming Chen
In molecular dynamics (MD) simulations, accessing transition probabilities between states is crucial for understanding kinetic information, such as reaction paths and rates. Howeve…