On the Power and Challenges of Atomistic Molecular Dynamics to Investigate RNA Molecules
RNA molecules play a vital role in biological processes within the cell, with significant
implications for science and medicine. Notably, the biological functions exerted by specific …
implications for science and medicine. Notably, the biological functions exerted by specific …
Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles
Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA
structure. A number of forward models that relate measured SAXS intensities and structural …
structure. A number of forward models that relate measured SAXS intensities and structural …
[HTML][HTML] Benchmarking predictive methods for small-angle X-ray scattering from atomic coordinates of proteins using maximum likelihood consensus data
J Trewhella, P Vachette, AH Larsen - IUCrJ, 2024 - journals.iucr.org
Stimulated by informal conversations at the XVII International Small Angle Scattering (SAS)
conference (Traverse City, 2017), an international team of experts undertook a round-robin …
conference (Traverse City, 2017), an international team of experts undertook a round-robin …
Connecting diffraction experiments and network analysis tools for the study of hydrogen-bonded networks
A self-consistent scheme is presented that is applicable for revealing details of the
microscopic structure of hydrogen-bonded liquids, including the description of the hydrogen …
microscopic structure of hydrogen-bonded liquids, including the description of the hydrogen …
Photoactivation of Drosophila melanogaster cryptochrome through sequential conformational transitions
O Berntsson, R Rodriguez, L Henry, MR Panman… - Science …, 2019 - science.org
Cryptochromes are blue-light photoreceptor proteins, which provide input to circadian
clocks. The cryptochrome from Drosophila melanogaster (Dm Cry) modulates the …
clocks. The cryptochrome from Drosophila melanogaster (Dm Cry) modulates the …
Comparing state-of-the-art approaches to back-calculate SAXS spectra from atomistic molecular dynamics simulations
M Bernetti, G Bussi - The European Physical Journal B, 2021 - Springer
Small-angle X-ray scattering (SAXS) experiments are arising as an effective instrument in
the structural characterization of biomolecules in solution. However, they suffer from limited …
the structural characterization of biomolecules in solution. However, they suffer from limited …
Mutual effects between single-stranded DNA conformation and Na+–Mg 2+ ion competition in mixed salt solutions
The ion-dependence of single-stranded DNA (ssDNA) conformational changes has attracted
growing attention because of its biological and technological importance. Although single …
growing attention because of its biological and technological importance. Although single …
Salt dependence of A-form RNA duplexes: Structures and implications
The biological functions of RNA range from gene regulation through catalysis and depend
critically on its structure and flexibility. Conformational variations of flexible, non-base-paired …
critically on its structure and flexibility. Conformational variations of flexible, non-base-paired …
In Situ X-ray Scattering Observation and Collective Analyses of the Complete Formation Process of Mesoporous SBA-15
The dynamic formation process of mesoporous silica (SBA-15) using hexane as a swelling
agent is fully elucidated through the in situ small-angle X-ray scattering (SAXS) technique in …
agent is fully elucidated through the in situ small-angle X-ray scattering (SAXS) technique in …
Predicting solution scattering patterns with explicit-solvent molecular simulations
L Chatzimagas, JS Hub - Methods in Enzymology, 2022 - Elsevier
Small-angle X-ray or neutron scattering (SAXS/SANS/SAS) is widely used to obtain
structural information on biomolecules or soft-matter complexes in solution. Deriving a …
structural information on biomolecules or soft-matter complexes in solution. Deriving a …