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Publication Detail
Differentiable molecular simulation can learn all the parameters in a coarse-grained force field for proteins
  • Publication Type:
    Journal article
  • Authors:
    Greener JG, Jones DT
  • Publication date:
    02/09/2021
  • Journal:
    PLOS ONE
  • Volume:
    16
  • Issue:
    9
  • Article number:
    e0256990
  • Status:
    Published
  • Country:
    United States
  • PII:
    PONE-D-21-12960
  • Language:
    English
  • Notes:
    This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
Abstract
Finding optimal parameters for force fields used in molecular simulation is a challenging and time-consuming task, partly due to the difficulty of tuning multiple parameters at once. Automatic differentiation presents a general solution: run a simulation, obtain gradients of a loss function with respect to all the parameters, and use these to improve the force field. This approach takes advantage of the deep learning revolution whilst retaining the interpretability and efficiency of existing force fields. We demonstrate that this is possible by parameterising a simple coarse-grained force field for proteins, based on training simulations of up to 2,000 steps learning to keep the native structure stable. The learned potential matches chemical knowledge and PDB data, can fold and reproduce the dynamics of small proteins, and shows ability in protein design and model scoring applications. Problems in applying differentiable molecular simulation to all-atom models of proteins are discussed along with possible solutions and the variety of available loss functions. The learned potential, simulation scripts and training code are made available at https://github.com/psipred/cgdms.
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