Principles of protein structural ensemble determination
Highlights•The principles of protein structural ensemble determination are described.•The
use of experimental data averaged over multiple states is analysed.•Approaches for …
use of experimental data averaged over multiple states is analysed.•Approaches for …
Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins
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 …
high level of structural heterogeneity and are best described by ensembles consisting of …
Combining experiments and simulations using the maximum entropy principle
A key component of computational biology is to compare the results of computer modelling
with experimental measurements. Despite substantial progress in the models and …
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 …
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 …
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 …
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
Accurate mechanistic description of structural changes in biomolecules is an increasingly
important topic in structural and chemical biology. Markov models have emerged as a …
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) …
the wide interest in deriving accurate solution ensembles of IDPs. Molecular dynamics (MD) …
ENCORE: software for quantitative ensemble comparison
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 …
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
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 …
molecular dynamics are not accurate enough to describe the conformational ensemble of …