3 papers
physics.chem-ph2026
MDArena: Evaluating Coding Agents on Realistic Molecular Dynamics Workflows
Nithishwer Mouroug Anand, Wei-Tse Hsu, Kyle Vaccaro +6
Accelerating scientific discovery is among the most consequential applications of AI, and computational biomolecular simulation stands out as a particularly promising target within…
cs.LG2025
Can AI-predicted complexes teach machine learning to compute drug binding affinity?
Wei-Tse Hsu, Savva Grevtsev, Thomas Douglas +2
We evaluate the feasibility of using co-folding models for synthetic data augmentation in training machine learning-based scoring functions (MLSFs) for binding affinity prediction.…
physics.chem-ph2024
Multiple Topology Replica Exchange of Expanded Ensembles (MT-REXEE) for Multidimensional Alchemical Calculations
Anika J. Friedman, Wei-Tse Hsu, Michael R. Shirts
Relative free energy calculations are now widely used in academia and industry, but the accuracy is often limited by poor sampling of the complexes conformational ensemble. To addr…