How to learn from inconsistencies: Integrating molecular simulations with experimental data.

Progress in Molecular Biology and Translational Science
Simone OrioliKresten Lindorff-Larsen

Abstract

Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modeling tool to interpret experimental measurements, and to use experimental data to refine our biophysical models. Thus, explicit integration and synergy between molecular simulations and experiments is fundamental for furthering our understanding of biological processes. This is especially true in the case where discrepancies between measured and simulated observables emerge. In this chapter, we provide an overview of some of the core ideas behind methods that were developed to improve the consistency between experimental information and numerical predictions. We distinguish between situations where experiments are used to refine our understanding and models of specific systems, and situations where experiments are used more generally to refine transferable models. We discuss different philosophies and attempt to unify them in a single framework. Until now, such integration between experiments and simulations have mostly been applied to equilibrium data, and we discuss more recent developments aime...Continue Reading

Citations

Jun 24, 2020·The Journal of Chemical Physics·Thorben FröhlkingGiovanni Bussi
Jul 1, 2020·Biochemical Society Transactions·Andy M LauArgyris Politis
Oct 22, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Reinier CárdenasCarlos Amero
Jan 23, 2021·PLoS Computational Biology·Giulio TeseiKresten Lindorff-Larsen
Jan 23, 2021·ELife·Dennis V PedersenGregers R Andersen
Dec 31, 2020·Proceedings of the National Academy of Sciences of the United States of America·Z Faidon BrotzakisPeter G Bolhuis
May 11, 2021·Frontiers in Molecular Biosciences·Mustapha Carab AhmedKresten Lindorff-Larsen
May 29, 2021·Frontiers in Molecular Biosciences·Vincent A VoelzRobert M Raddi
Jul 23, 2021·Journal of Chemical Theory and Computation·Felix KümmererKresten Lindorff-Larsen
Dec 29, 2020·The Journal of Physical Chemistry. B·Nicholas E Jackson
Oct 31, 2021·Proceedings of the National Academy of Sciences of the United States of America·Giulio TeseiKresten Lindorff-Larsen

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