scholarly journals Improving Coarse-Grained Protein Force Fields with Small-Angle X-ray Scattering Data

2019 ◽  
Vol 123 (5) ◽  
pp. 1026-1034 ◽  
Author(s):  
Andrew P. Latham ◽  
Bin Zhang
Keyword(s):  
Small Angle ◽  
Force Fields ◽  
Coarse Grained ◽  
Scattering Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Protein Force Fields ◽  
Ray Scattering

scholarly journals Biasing RNA coarse-grained folding simulations with Small--Angle X--ray Scattering (SAXS) data

2021 ◽  
Author(s):  
Liuba Mazzanti ◽  
Lina Alferkh ◽  
Elisa Frezza ◽  
Samuela Pasquali
Keyword(s):  
High Resolution ◽  
Small Angle ◽  
Conformational Space ◽  
Coarse Grained ◽  
Scattering Data ◽  
Saxs Data ◽  
X Ray ◽  
Rna Molecules ◽  
X Ray Scattering ◽  
Ray Scattering

RNA molecules can easily adopt alternative structures in response to different environmental conditions. As a result, a molecule's energy landscape is rough and can exhibits a multitude of deep basins. In the absence of a high-resolution structure, Small Angle X-ray Scattering data (SAXS) can narrow down the conformational space available to the molecule and be used in conjunction with physical modeling to obtain high-resolution putative structures to be further tested by experiments. Because of the low-resolution of this data, it is natural to implement the integration of SAXS data into simulations using a coarse-grained representation of the molecule, allowing for much wider searches and faster evaluation of SAXS theoretical intensity curves than with atomistic models. We present here the theoretical framework and the implementation of a simulation approach based on our coarse-grained model HiRE-RNA combined with SAXS evaluations "on-the-fly" leading the simulation toward conformations agreeing with the scattering data, starting from partially folded structures as the ones that can easily be obtained from secondary structures predictions based tools. We show on three benchmark systems how our approach can successfully achieve high-resolution structures with remarkable similarity with the native structure recovering not only the overall shape, as imposed by SAXS data, but also the details of initially missing base pairs.

scholarly journals Global Small-Angle X-ray Scattering Data Analysis of Triacylglycerols in the Molten State (Part I)

2018 ◽  
Vol 122 (45) ◽  
pp. 10320-10329 ◽  
Author(s):  
Amin Sadeghpour ◽  
Marjorie Ladd Parada ◽  
Josélio Vieira ◽  
Megan Povey ◽  
Michael Rappolt
Keyword(s):  
Data Analysis ◽  
Small Angle ◽  
Scattering Data ◽  
Molten State ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

scholarly journals Molecular Structure of Sphingomyelin in Fluid Phase Bilayers Determined by the Joint Analysis of Small-Angle Neutron and X-ray Scattering Data

2020 ◽  
Vol 124 (25) ◽  
pp. 5186-5200 ◽  
Author(s):  
Milka Doktorova ◽  
Norbert Kučerka ◽  
Jacob J. Kinnun ◽  
Jianjun Pan ◽  
Drew Marquardt ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Small Angle ◽  
Fluid Phase ◽  
Scattering Data ◽  
Joint Analysis ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering
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