Journal: Biophys J / Year: 2018 Title: Machine Learning Methods for X-Ray Scattering Data Analysis from Biomacromolecular Solutions. Authors: Daniel Franke / Cy M Jeffries / Dmitri I Svergun / Abstract: Small-angle x-ray scattering (SAXS) of biological macromolecules in solutions is a widely employed method in structural biology. SAXS patterns include information about the overall shape and low- ...Small-angle x-ray scattering (SAXS) of biological macromolecules in solutions is a widely employed method in structural biology. SAXS patterns include information about the overall shape and low-resolution structure of dissolved particles. Here, we describe how to transform experimental SAXS patterns to feature vectors and how a simple k-nearest neighbor approach is able to retrieve information on overall particle shape and maximal diameter (D) as well as molecular mass directly from experimental scattering data. Based on this transformation, we develop a rapid multiclass shape-classification ranging from compact, extended, and flat categories to hollow and random-chain-like objects. This classification may be employed, e.g., as a decision block in automated data analysis pipelines. Further, we map protein structures from the Protein Data Bank into the classification space and, in a second step, use this mapping as a data source to obtain accurate estimates for the structural parameters (D, molecular mass) of the macromolecule under study based on the experimental scattering pattern alone, without inverse Fourier transform for D. All methods presented are implemented in a Fortran binary DATCLASS, part of the ATSAS data analysis suite, available on Linux, Mac, and Windows and free for academic use.
Contact author
Cy M Jeffries (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)
Instrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.124 Å / Dist. spec. to detc.: 3.1 mm
Detector
Name: Pilatus 2M
Scan
Title: Folded ribonuclease A (RNAse) / Measurement date: Jul 29, 2013 / Storage temperature: 10 °C / Cell temperature: 10 °C / Exposure time: 0.05 sec. / Number of frames: 2 / Unit: 1/nm /
Min
Max
Q
0.0536
3.4949
Distance distribution function P(R)
Sofotware P(R): GNOM 4.6 / Number of points: 427 /
Min
Max
Q
0.08254
3.488
P(R) point
14
440
R
0
5.56
Result
Type of curve: single_conc
Experimental
Standard
Porod
MW
17.4 kDa
17.4 kDa
10 kDa
Volume
-
-
15.9 nm3
P(R)
Guinier
Guinier error
Forward scattering, I0
626.3
629.71
2.21
Radius of gyration, Rg
1.61 nm
1.61 nm
0.06
Min
Max
D
-
5.56
Guinier point
22
379
+
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