scholarly journals Model Reconstruction from Small-Angle X-Ray Scattering Data Using Deep Learning Methods

iScience ◽  
2020 ◽  
Vol 23 (3) ◽  
pp. 100906 ◽  
Author(s):  
Hao He ◽  
Can Liu ◽  
Haiguang Liu
2019 ◽  
Author(s):  
Hao He ◽  
Can Liu ◽  
Haiguang Liu

AbstractWe present an algorithm based on a deep learning method for model reconstruction from small angle X-ray scattering (SAXS) data. An auto-encoder for protein 3D models was trained to compress 3D shape information into vectors of a 200-dimensional latent space, and the vectors are optimized using genetic algorithms to build 3D models that are consistent with the scattering data. The algorithm was implemented using Python with the TensorFlow framework and tested with experimental data, demonstrating capacity and robustness of accurate model reconstruction even without using prior model size information.SynopsisA deep learning method based on the auto-encoder framework for model reconstruction from small angle scattering data


2018 ◽  
Vol 122 (45) ◽  
pp. 10320-10329 ◽  
Author(s):  
Amin Sadeghpour ◽  
Marjorie Ladd Parada ◽  
Josélio Vieira ◽  
Megan Povey ◽  
Michael Rappolt

2020 ◽  
Vol 124 (25) ◽  
pp. 5186-5200 ◽  
Author(s):  
Milka Doktorova ◽  
Norbert Kučerka ◽  
Jacob J. Kinnun ◽  
Jianjun Pan ◽  
Drew Marquardt ◽  
...  

2018 ◽  
Vol 2 (1) ◽  
pp. 69-79 ◽  
Author(s):  
Martin A. Schroer ◽  
Dmitri I. Svergun

Small-angle X-ray scattering (SAXS) has become a streamline method to characterize biological macromolecules, from small peptides to supramolecular complexes, in near-native solutions. Modern SAXS requires limited amounts of purified material, without the need for labelling, crystallization, or freezing. Dedicated beamlines at modern synchrotron sources yield high-quality data within or below several milliseconds of exposure time and are highly automated, allowing for rapid structural screening under different solutions and ambient conditions but also for time-resolved studies of biological processes. The advanced data analysis methods allow one to meaningfully interpret the scattering data from monodisperse systems, from transient complexes as well as flexible and heterogeneous systems in terms of structural models. Especially powerful are hybrid approaches utilizing SAXS with high-resolution structural techniques, but also with biochemical, biophysical, and computational methods. Here, we review the recent developments in the experimental SAXS practice and in analysis methods with a specific focus on the joint use of SAXS with complementary methods.


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