scholarly journals Z-score to evaluate the absolute quality of macromolecular models based on SAXS data

2018 ◽  
Author(s):  
Dmytro Guzenko ◽  
Sergei V. Strelkov
Keyword(s):  
Goodness Of Fit ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Statistical Criterion ◽  
Biological Macromolecules ◽  
Z Score ◽  
Saxs Data ◽  
X Ray Scattering ◽  
Saxs Curve

Small-angle X-ray scattering (SAXS) is a highly popular technique to assess the native three-dimensional structure of biological macromolecules in solution. Here we introduce a statistical criterion, Z-score, as a novel quality measure of SAXS-based structural models which positively correlates with data quality. We propose that, besides a goodness-of-fit (GOF) measure such as reduced χ2, the Z-score reflecting the ability of a given SAXS curve to differentiate between possible models should always be reported.

scholarly journals Geometric Constraints for the Phase Problem in X-Ray Crystallography

10.29007/p2pj ◽  
2018 ◽  
Author(s):  
Corinna Heldt ◽  
Alexander Bockmayr
Keyword(s):  
Electron Density Distribution ◽  
Fourier Coefficients ◽  
Three Dimensional ◽  
Geometric Constraints ◽  
Dimensional Structure ◽  
Biological Macromolecules ◽  
Phase Problem ◽  
X Ray ◽  
X Ray Crystallography

X-ray crystallography is one of the main methods to establish the three-dimensional structure of biological macromolecules. In an X-ray experiment, one can measure only the magnitudes of the complex Fourier coefficients of the electron density distribution under study, but not their phases. The problem of recovering the lost phases is called the phase problem. Building on earlier work by Lunin/Urzhumtsev/Bockmayr, we extend their constraint-based approach to the phase problem by adding further 0-1 linear programming constraints. These constraints describe geometric properties of proteins and increase the quality of the solutions. The approach has been implemented using SCIP and CPLEX, first computational results are presented here.

Structural refinement by restrained molecular-dynamics algorithm with small-angle X-ray scattering constraints for a biomolecule

2004 ◽  
Vol 37 (1) ◽  
pp. 103-109 ◽  
Author(s):  
Masaki Kojima ◽  
Alexander A. Timchenko ◽  
Junichi Higo ◽  
Kazuki Ito ◽  
Hiroshi Kihara ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Small Angle ◽  
Protein Structures ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Saxs Curve ◽  
Restrained Molecular Dynamics ◽  
Ray Scattering

A new algorithm to refine protein structures in solution from small-angle X-ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared differences between calculated and observed SAXS intensities was used as a constraint energy function, and the calculation was started from given atomic coordinates, such as those of the crystal. In order to reduce the contribution of the hydration effect to the deviation from the experimental (objective) curve during the dynamics, and purely as an estimate of the efficiency of the algorithm, the calculation was first performed assuming the SAXS curve corresponding to the crystal structure as the objective curve. Next, the calculation was carried out with `real' experimental data, which yielded a structure that satisfied the experimental SAXS curve well. The SAXS data for ribonuclease T1, a single-chain globular protein, were used for the calculation, along with its crystal structure. The results showed that the present algorithm was very effective in the refinement and adjustment of the initial structure so that it could satisfy the objective SAXS data.

Three-dimensional structure of the calcite–water interface by surface X-ray scattering

2004 ◽  
Vol 573 (2) ◽  
pp. 191-203 ◽  
Author(s):  
P. Geissbühler ◽  
P. Fenter ◽  
E. DiMasi ◽  
G. Srajer ◽  
L.B. Sorensen ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Interface ◽  
X Ray ◽  
Three Dimensional Structure ◽  
X Ray Scattering ◽  
Ray Scattering

Quality control of protein standards for molecular mass determinations by small-angle X-ray scattering

2010 ◽  
Vol 43 (2) ◽  
pp. 237-243 ◽  
Author(s):  
Shuji Akiyama
Keyword(s):  
Quality Control ◽  
Molecular Mass ◽  
Small Angle ◽  
Biological Macromolecules ◽  
Average Deviation ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Standard Quality ◽  
Ray Scattering

Small-angle X-ray scattering (SAXS) is a powerful technique with which to evaluate the size and shape of biological macromolecules in solution. Forward scattering intensity normalized relative to the particle concentration,I(0)/c, is useful as a good measure of molecular mass. A general method for deducing the molecular mass from SAXS data is to determine the ratio ofI(0)/cof a target protein to that of a standard protein with known molecular mass. The accuracy of this interprotein calibration is affected considerably by the monodispersity of the prepared standard, as well as by the precision in estimating its concentration. In the present study, chromatographic fractionation followed by hydrodynamic characterization is proposed as an effective procedure by which to prepare a series of monodispersed protein standards. The estimation of molecular mass within an average deviation of 8% is demonstrated using monodispersed bovine serum albumin as a standard. The present results demonstrate the importance of protein standard quality control in order to take full advantage of interprotein calibration.

scholarly journals Supercritical CO2extraction of porogen phase: An alternative route to nanoporous dielectrics

2004 ◽  
Vol 19 (11) ◽  
pp. 3224-3233 ◽  
Author(s):  
J.A. Lubguban ◽  
S. Gangopadhyay ◽  
B. Lahlouh ◽  
T. Rajagopalan ◽  
N. Biswas ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Selective Extraction ◽  
Porous Structures ◽  
Saxs Data ◽  
3D Images ◽  
X Ray ◽  
X Ray Scattering ◽  
Through Diffusion ◽  
Organosilicate Thin Films ◽  
Poly Propylene

We present a supercritical CO2(SCCO2) process for the preparation of nanoporous organosilicate thin films for ultralow dielectric constant materials. The porous structure was generated by SCCO2extraction of a sacrificial poly(propylene glycol) (PPG) from a nanohybrid film, where the nanoscopic domains of PPG porogen are entrapped within the crosslinked poly(methylsilsesquioxane) (PMSSQ) matrix. As a comparison, porous structures generated by both the usual thermal decomposition (at approximately 450 °C) and by a SCCO2process for 25 and 55 wt% porogen loadings were evaluated. It is found that the SCCO2process is effective in removing the porogen phase at relatively low temperatures (<200 °C) through diffusion of the supercritical fluid into the phase-separated nanohybrids and selective extraction of the porogen phase. Pore morphologies generated from the two methods are compared from representative three-dimensional (3D) images built from small-angle x-ray scattering (SAXS) data.

scholarly journals Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein–protein interactions

2019 ◽  
Vol 47 (W1) ◽  
pp. W331-W337 ◽  
Author(s):  
Ankit A Roy ◽  
Abhilesh S Dhawanjewar ◽  
Parichit Sharma ◽  
Gulzar Singh ◽  
M S Madhusudhan
Keyword(s):  
Protein Interactions ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Optimal Number ◽  
Dimensional Structure ◽  
Side Chain ◽  
Interface Residue ◽  
Z Score ◽  
Protein Protein Interactions ◽  
Residue Contacts

Abstract Our web server, PIZSA (http://cospi.iiserpune.ac.in/pizsa), assesses the likelihood of protein–protein interactions by assigning a Z Score computed from interface residue contacts. Our score takes into account the optimal number of atoms that mediate the interaction between pairs of residues and whether these contacts emanate from the main chain or side chain. We tested the score on 174 native interactions for which 100 decoys each were constructed using ZDOCK. The native structure scored better than any of the decoys in 146 cases and was able to rank within the 95th percentile in 162 cases. This easily outperforms a competing method, CIPS. We also benchmarked our scoring scheme on 15 targets from the CAPRI dataset and found that our method had results comparable to that of CIPS. Further, our method is able to analyse higher order protein complexes without the need to explicitly identify chains as receptors or ligands. The PIZSA server is easy to use and could be used to score any input three-dimensional structure and provide a residue pair-wise break up of the results. Attractively, our server offers a platform for users to upload their own potentials and could serve as an ideal testing ground for this class of scoring schemes.

COMPUTER SIMULATION OF BIOLOGICAL MACROMOLECULES IN GENERALIZED ENSEMBLES

1999 ◽  
Vol 10 (08) ◽  
pp. 1521-1530 ◽  
Author(s):  
ULRICH H. E. HANSMANN
Keyword(s):  
Computer Simulation ◽  
Protein Folding ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Biological Macromolecules ◽  
Three Dimensional Structure ◽  
Ensemble Techniques ◽  
Folding Simulations ◽  
Protein Models ◽  
Structure Of Proteins

For many years the emphasis in protein-folding simulations has been laid as to how to predict the three-dimensional structure of proteins. Only recently has there be a shift in interest towards the thermodynamics of folding. We show that generalized-ensemble techniques are well suited to study both questions for realistic protein models.

scholarly journals CLABAUTAIR: a new algorithm for retrieving three-dimensional cloud structure from airborne microphysical measurements

2005 ◽  
Vol 5 (9) ◽  
pp. 2333-2340 ◽  
Author(s):  
R. Scheirer ◽  
S. Schmidt
Keyword(s):  
Three Dimensional ◽  
Lower Troposphere ◽  
Dimensional Structure ◽  
East Anglia ◽  
Airborne Measurements ◽  
Microphysical Parameters ◽  
Large Eddy ◽  
Measured Probability ◽  
Dimensional Distribution

Abstract. A new algorithm is presented to reproduce the three-dimensional structure of clouds from airborne measurements of microphysical parameters. Data from individual flight legs are scanned for characteristic patterns, and the autocorrelation functions for several directions are used to extrapolate the observations along the flight path to a full three-dimensional distribution of the cloud field. Thereby, the mean measured profiles of microphysical parameters are imposed to the cloud field by mapping the measured probability density functions onto the model layers. The algorithm was tested by simulating flight legs through synthetic clouds (by means of Large Eddy Simulations (LES)) and applied to a stratocumulus cloud case measured during the first field experiment of the EC project INSPECTRO (INfluence of clouds on the SPECtral actinic flux in the lower TROposphere) in East Anglia, UK. The number and position of the flight tracks determine the quality of the retrieved cloud field. If they provide a representative sample of the entire field, the derived pattern closely resembles the statistical properties of the real cloud field.

scholarly journals Reconstruction of crystal shapes by X-ray nanodiffraction from three-dimensional superlattices

2014 ◽  
Vol 47 (6) ◽  
pp. 2030-2037 ◽  
Author(s):  
Mojmír Meduňa ◽  
Claudiu V. Falub ◽  
Fabio Isa ◽  
Daniel Chrastina ◽  
Thomas Kreiliger ◽  
...  
Keyword(s):  
Structural Model ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Semiconductor Layer ◽  
Dimensional Structure ◽  
Solid State Lasers ◽  
X Ray ◽  
Nondestructive Imaging ◽  
Low Dimensional

Quantitative nondestructive imaging of structural properties of semiconductor layer stacks at the nanoscale is essential for tailoring the device characteristics of many low-dimensional quantum structures, such as ultrafast transistors, solid state lasers and detectors. Here it is shown that scanning nanodiffraction of synchrotron X-ray radiation can unravel the three-dimensional structure of epitaxial crystals containing a periodic superlattice underneath their faceted surface. By mapping reciprocal space in all three dimensions, the superlattice period is determined across the various crystal facets and the very high crystalline quality of the structures is demonstrated. It is shown that the presence of the superlattice allows the reconstruction of the crystal shape without the need of any structural model.

Determining the shape and periodicity of nanostructures using small-angle X-ray scattering

2015 ◽  
Vol 48 (5) ◽  
pp. 1355-1363 ◽  
Author(s):  
Daniel F. Sunday ◽  
Scott List ◽  
Jasmeet S. Chawla ◽  
R. Joseph Kline
Keyword(s):  
Small Angle ◽  
Semiconductor Industry ◽  
Three Dimensional ◽  
Critical Dimension ◽  
Dimensional Structure ◽  
Critical Dimensions ◽  
X Ray ◽  
Line Shapes ◽  
X Ray Scattering ◽  
Ray Scattering

The semiconductor industry is exploring new metrology techniques capable of meeting the future requirement to characterize three-dimensional structure where the critical dimensions are less than 10 nm. X-ray scattering techniques are one candidate owing to the sub-Å wavelengths which are sensitive to internal changes in electron density. Critical-dimension small-angle X-ray scattering (CDSAXS) has been shown to be capable of determining the average shape of a line grating. Here it is used to study a set of line gratings patternedviaa self-aligned multiple patterning process, which resulted in a set of mirrored lines, where the individual line shapes were asymmetric. The spacing between lines was systematically varied by sub-nm shifts. The model used to simulate the scattering was developed in stages of increasing complexity in order to justify the large number of parameters included. Comparisons between the models at different stages of development demonstrate that the measurement can determine differences in line shapes within the superlattice. The shape and spacing between lines within a given set were determined to sub-nm accuracy. This demonstrates the potential for CDSAXS as a high-resolution nanostructure metrology tool.

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