Determination of domain structure of proteins from X-ray solution scattering.

By Dmitri I. Svergun, M. Petoukhov, M. Koch. Biophysical Journal, 2001

1,385 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/7f91d8886da2a425a327cfdada2963b3c8f0577e

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Citations in the corpus

RNF168 ubiquitinates K13-15 on H2A/H2AX to drive DNA damage signaling. (2012, methodology): “analyzed using the ATSAS software package (Svergun et al., 2001).”
How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans (2017, methodology): “The low-resolution shape of BT4661 and BT4661L in solution was determined ab initio from the merged scattering curve using the program GASBOR (39).”
Choice of data-collection parameters based on statistic modelling. (2003, background): “…the temperature factors, the pattern of spherically averaged squared structure-factor magnitudes (the ®rst moment of the Wilson distribution) for different protein molecules differs signi®cantly to a resolution of d = 7±5 AÊ , but appears to converge at higher resolution (Svergun et al., 2001).”
Global rigid body modeling of macromolecular complexes against small-angle scattering data. (2005, methodology): “A feasible alternative to the exhaustive search methods is simulated annealing (SA) (26), a technique used for global minimization of multivariant functions in different fields, and, in particular, for ab initio small-angle x-ray scattering (SAXS) data analysis (10,11,27).”
How Random are Intrinsically Disordered Proteins? A Small Angle Scattering Perspective (2012, methodology): “DAILA_GA, for example, uses a genetic algorithm [67], whereas SAXS3D uses a Monte Carlo-type reconstruction algorithm [68], and the program suite DAMMIN/ DAMMIF/MONSA/GASBOR uses a simulated annealing procedure [69, 70].”
LGP2 is a positive regulator of RIG-I– and MDA5-mediated antiviral responses (2010, methodology): “Low-resolution models of both tetherin samples were simulated by the program DAMMIN (Svergun, 1999) and GASBOR (Svergun et al., 2001), which resulted in similar elongated structures.”
Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS) (2009, methodology): “New algorithms have been developed that can identify accurate shapes and assemblies based on the scattering dat”
DAMMIF, a program for rapid ab-initio shape determination in small-angle scattering (2009, neutral): “For the analysis of higher-resolution data from small (less than 30 kDa) proteins, where the contribution from the internal structure is essential, other programs like GASBOR (Svergun et al., 2001) may be more appropriate for abinitio analysis than the shape determination algorithms.”
Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy (2018, methodology): “Molecular envelope calculations were performed using GASBOR (see also Supplement 1 for a brief outline of SAXS fundamentals).(36)”
ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions (2017, methodology): “Also note that, while it is possible to treat DR models of GASBOR in this manner, the DRs would be broken into dummy beads and information may be lost.”
New developments in the ATSAS program package for small-angle scattering data analysis (2012, neutral): “The ab initio program GASBOR represents the protein structure using a fixed number of dummy residues (DRs) and uses a simulated annealing (SA) protocol to obtain a spatial distribution of DRs that fits the experimental data (Svergun et al., 2001).”
ATSAS 2.1, a program package for small‐angle scattering data analysis (2006, neutral): “The most frequently used parameters are transmitted from a string of keys with key values, similar to DAMMIN and GASBOR.”