Simulation and Retargeting of Complex Multi-Character Interactions
Yunbo Zhang, Deepak Gopinath, Yuting Ye, Jessica Hodgins, Greg Turk, Jungdam Won
International Conference on Learning Representations (ICLR)
We propose an energy-based model (EBM) of protein conformations that operates at atomic scale. The model is trained solely on crystallized protein data. By contrast, existing approaches for scoring conformations use energy functions that incorporate knowledge of physical principles and features that are the complex product of several decades of research and tuning. To evaluate the model, we benchmark on the rotamer recovery task, the problem of predicting the conformation of a side chain from its context within a protein structure, which has been used to evaluate energy functions for protein design. The model achieves performance close to that of the Rosetta energy function, a state-of-the-art method widely used in protein structure prediction and design. An investigation of the model’s outputs and hidden representations finds that it captures physicochemical properties relevant to protein energy.
Yunbo Zhang, Deepak Gopinath, Yuting Ye, Jessica Hodgins, Greg Turk, Jungdam Won
Harrison Jesse Smith, Qingyuan Zheng, Yifei Li, Somya Jain, Jessica K. Hodgins
Simran Arora, Patrick Lewis, Angela Fan, Jacob Kahn, Christopher Ré