Principles of protein structural ensemble determination

M Bonomi, GT Heller, C Camilloni… - Current opinion in …, 2017 - Elsevier
Highlights•The principles of protein structural ensemble determination are described.•The
use of experimental data averaged over multiple states is analysed.•Approaches for …

Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins

FE Thomasen, K Lindorff-Larsen - Biochemical Society …, 2022 - portlandpress.com
Intrinsically disordered proteins (IDPs) and multidomain proteins with flexible linkers show a
high level of structural heterogeneity and are best described by ensembles consisting of …

Combining experiments and simulations using the maximum entropy principle

W Boomsma, J Ferkinghoff-Borg… - PLoS computational …, 2014 - journals.plos.org
A key component of computational biology is to compare the results of computer modelling
with experimental measurements. Despite substantial progress in the models and …

An introduction to the maximum entropy approach and its application to inference problems in biology

A De Martino, D De Martino - Heliyon, 2018 - cell.com
A cornerstone of statistical inference, the maximum entropy framework is being increasingly
applied to construct descriptive and predictive models of biological systems, especially …

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

S Orioli, AH Larsen, S Bottaro… - Progress in Molecular …, 2020 - Elsevier
Molecular simulations and biophysical experiments can be used to provide independent
and complementary insights into the molecular origin of biological processes. A particularly …

The nuclear Overhauser effect from a quantitative perspective

B Vögeli - Progress in nuclear magnetic resonance spectroscopy, 2014 - Elsevier
The nuclear Overhauser enhancement or effect (NOE) is the most important measure in
liquid-state NMR with macromolecules. Thus, the NOE is the subject of numerous reviews …

Combining experimental and simulation data of molecular processes via augmented Markov models

S Olsson, H Wu, F Paul… - Proceedings of the …, 2017 - National Acad Sciences
Accurate mechanistic description of structural changes in biomolecules is an increasingly
important topic in structural and chemical biology. Markov models have emerged as a …

SAXS-restrained ensemble simulations of intrinsically disordered proteins with commitment to the principle of maximum entropy

MR Hermann, JS Hub - Journal of chemical theory and …, 2019 - ACS Publications
Intrinsically disordered proteins (IDPs) play key roles in biology and disease, rationalizing
the wide interest in deriving accurate solution ensembles of IDPs. Molecular dynamics (MD) …

ENCORE: software for quantitative ensemble comparison

M Tiberti, E Papaleo, T Bengtsen… - PLoS computational …, 2015 - journals.plos.org
There is increasing evidence that protein dynamics and conformational changes can play an
important role in modulating biological function. As a result, experimental and computational …

Combining simulations and solution experiments as a paradigm for RNA force field refinement

A Cesari, A Gil-Ley, G Bussi - Journal of chemical theory and …, 2016 - ACS Publications
Recent computational efforts have shown that the current potential energy models used in
molecular dynamics are not accurate enough to describe the conformational ensemble of …