Dataset Information

Accuracy of the Kirchhoff-approximation and Kirchhoff-ray-mode fish swimbladder acoustic scattering models.

ABSTRACT: The acoustic backscatter from pressure release prolate spheroids and a three-dimensional representation of a fish swimbladder (Chilean jack mackerel, Trachurus symmetricus murphyi) was calculated using four target strength models (Kirchhoff-approximation, Kirchhoff-ray-mode, finite element solution of the Helmholtz equation, and prolate-spheroid-modal-series). Smoothly varying errors were found in the Kirchhoff-approximation and Kirchhoff-ray-mode model results when compared to the other models, and provide objective criteria for constraining the use of the KA and KRM models. A generic correction technique is also proposed for the prolate spheroid estimates and tentatively tested on a jack mackerel swimbladder, resulting in improvements to the target strength estimates from the Kirchhoff-approximation and Kirchhoff-ray-mode models.

SUBMITTER: Macaulay GJ

PROVIDER: S-EPMC3653833 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Publications

Accuracy of the Kirchhoff-approximation and Kirchhoff-ray-mode fish swimbladder acoustic scattering models.

Macaulay Gavin J GJ Peña Héctor H Fässler Sascha M M SM Pedersen Geir G Ona Egil E

PloS one 20130514 5

The acoustic backscatter from pressure release prolate spheroids and a three-dimensional representation of a fish swimbladder (Chilean jack mackerel, Trachurus symmetricus murphyi) was calculated using four target strength models (Kirchhoff-approximation, Kirchhoff-ray-mode, finite element solution of the Helmholtz equation, and prolate-spheroid-modal-series). Smoothly varying errors were found in the Kirchhoff-approximation and Kirchhoff-ray-mode model results when compared to the other models, ...[more]

PMID: 23691146

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Project description:BackgroundGenome sequencing projects have expanded the gap between the amount of known protein sequences and structures. The limitations of current high resolution structure determination methods make it unlikely that this gap will disappear in the near future. Small angle X-ray scattering (SAXS) is an established low resolution method for routinely determining the structure of proteins in solution. The purpose of this study is to develop a method for the efficient calculation of accurate SAXS curves from coarse-grained protein models. Such a method can for example be used to construct a likelihood function, which is paramount for structure determination based on statistical inference.ResultsWe present a method for the efficient calculation of accurate SAXS curves based on the Debye formula and a set of scattering form factors for dummy atom representations of amino acids. Such a method avoids the computationally costly iteration over all atoms. We estimated the form factors using generated data from a set of high quality protein structures. No ad hoc scaling or correction factors are applied in the calculation of the curves. Two coarse-grained representations of protein structure were investigated; two scattering bodies per amino acid led to significantly better results than a single scattering body.ConclusionWe show that the obtained point estimates allow the calculation of accurate SAXS curves from coarse-grained protein models. The resulting curves are on par with the current state-of-the-art program CRYSOL, which requires full atomic detail. Our method was also comparable to CRYSOL in recognizing native structures among native-like decoys. As a proof-of-concept, we combined the coarse-grained Debye calculation with a previously described probabilistic model of protein structure, TorusDBN. This resulted in a significant improvement in the decoy recognition performance. In conclusion, the presented method shows great promise for use in statistical inference of protein structures from SAXS data.

Dataset Information

Accuracy of the Kirchhoff-approximation and Kirchhoff-ray-mode fish swimbladder acoustic scattering models.

Publications

Accuracy of the Kirchhoff-approximation and Kirchhoff-ray-mode fish swimbladder acoustic scattering models.

Similar Datasets

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