Energy-based models for atomic-resolution protein conformations
- URL: http://arxiv.org/abs/2004.13167v1
- Date: Mon, 27 Apr 2020 20:45:12 GMT
- Title: Energy-based models for atomic-resolution protein conformations
- Authors: Yilun Du, Joshua Meier, Jerry Ma, Rob Fergus, Alexander Rives
- Abstract summary: We propose an energy-based model (EBM) of protein conformations that operates at atomic scale.
The model is trained solely on crystallized protein data.
An investigation of the model's outputs and hidden representations finds that it captures physicochemical properties relevant to protein energy.
- Score: 88.68597850243138
- License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
- Abstract: 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.
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