Issue 21, 2021

Molecular free energy optimization on a computational graph

Abstract

Free energy is arguably the most important property of molecular systems. Despite great progress in both its efficient estimation by scoring functions/potentials and more rigorous computation based on extensive sampling, we remain far from accurately predicting and manipulating biomolecular structures and their interactions. There are fundamental limitations, including accuracy of interaction description and difficulty of sampling in high dimensional space, to be tackled. Computational graph underlies major artificial intelligence platforms and is proven to facilitate training, optimization and learning. Combining autodifferentiation, coordinates transformation and generalized solvation free energy theory, we construct a computational graph infrastructure to realize seamless integration of fully trainable local free energy landscape with end to end differentiable iterative free energy optimization. This new framework drastically improves efficiency by replacing local sampling with differentiation. Its specific implementation in protein structure refinement achieves superb efficiency and competitive accuracy when compared with state of the art all-atom mainstream methods.

Graphical abstract: Molecular free energy optimization on a computational graph

Supplementary files

Article information

Article type
Paper
Submitted
23 Feb 2021
Accepted
26 Mar 2021
First published
06 Apr 2021
This article is Open Access
Creative Commons BY-NC license

RSC Adv., 2021,11, 12929-12937

Molecular free energy optimization on a computational graph

X. Cao and P. Tian, RSC Adv., 2021, 11, 12929 DOI: 10.1039/D1RA01455B

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