Variational scheme to compute protein reaction pathways using atomistic force fields with explicit solvent

Physical Review Letters
Silvio a BeccaraPietro Faccioli

Abstract

We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding, using state of the art all-atom force fields in explicit solvent. We test this method against MD simulations of the folding of an α and a β protein performed with the same all-atom force field on the Anton supercomputer. We find that our approach yields results consistent with those of MD simulations, at a computational cost orders of magnitude smaller.

References

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Feb 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Silvio A BeccaraPietro Faccioli
Jul 24, 2012·Proceedings of the National Academy of Sciences of the United States of America·Stefano PianaDavid E Shaw
Apr 5, 2013·PLoS Computational Biology·Silvio a BeccaraPietro Faccioli
Oct 15, 2014·Proceedings of the National Academy of Sciences of the United States of America·Giorgia CazzolliPatrick L Wintrode

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Citations

Nov 19, 2015·Journal of Chemical Theory and Computation·Lorenzo BoninsegnaCecilia Clementi
Apr 4, 2015·Physical Chemistry Chemical Physics : PCCP·Simone TaioliMarco Garavelli
Nov 13, 2019·The Journal of Biological Chemistry·Anne GershensonPatrick L Wintrode
Jul 12, 2019·PLoS Pathogens·Giovanni SpagnolliJesús R Requena
Oct 23, 2017·The Journal of Chemical Physics·S OrioliP Faccioli
Aug 24, 2018·The Journal of Chemical Physics·G BartolucciP Faccioli
Sep 19, 2020·PLoS Computational Biology·Luca TerruzziPietro Faccioli
Jan 19, 2019·International Journal of Molecular Sciences·Emanuel K Peter, Jiří Černý
Aug 16, 2017·The Journal of Chemical Physics·S OrioliP Faccioli
Jan 14, 2021·Communications Biology·Giovanni SpagnolliEmiliano Biasini
Jan 30, 2021·Physical Review Letters·Philipp HaukePietro Faccioli
Feb 2, 2021·The Journal of Biological Chemistry·Anne GershensonPatrick L Wintrode
Sep 2, 2021·JACS Au·Fabian DingfelderBenjamin Schuler

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