Reconstruction of Saxs Profiles From Protein Structures

Putnam, Daniel K.; Lowe, Edward W.; Meiler, Jens

doi:10.5936/csbj.201308006

Cited by 38 publications

(30 citation statements)

References 35 publications

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“…We also consider the masses of the atoms as a physical property in the protein shape function. The importance of adding mass to the shape function comes from the structure factors in X-ray scattering data [20]. Thus, adding the atomic masses to the shape function provides more reliable computed structure factors as we show later in this paper.…”

Section: Introductionmentioning

confidence: 80%

A new definition and properties of the similarity value between two protein structures

Fathi

2016

J Biol Phys

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Knowledge regarding the 3D structure of a protein provides useful information about the protein's functional properties. Particularly, structural similarity between proteins can be used as a good predictor of functional similarity. One method that uses the 3D geometrical structure of proteins in order to compare them is the similarity value (SV). In this paper, we introduce a new definition of the SV measure for comparing two proteins. To this end, we consider the mass of the protein's atoms and concentrate on the number of protein's atoms to be compared. This defines a new measure, called the weighted similarity value (WSV), adding physical properties to geometrical properties. We also show that our results are in good agreement with the results obtained by TM-SCORE and DALILITE. WSV can be of use in protein classification and in drug discovery.

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Section: Introductionmentioning

confidence: 80%

A new definition and properties of the similarity value between two protein structures

Fathi

2016

J Biol Phys

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“…Owing to the averaging procedure, it is necessary to consider only the modulus of the vector q, and one obtains the classical Debye formula (Putnam et al, 2013):…”

Section: Calculus Of Scattered Radiation a Brief Reviewmentioning

confidence: 99%

Calculation of two-dimensional scattering patterns for oriented systems

2017

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A versatile procedure to calculate two-dimensional scattering patterns of oriented systems is presented. The systems are represented by a set of dummy atoms with different scattering length densities, which allows the construction of very complex shapes either for single particles or for sets of particles. By the use of oriented pair distance distribution functions it is possible to perform a fast calculation of the scattering intensity from the oriented system in a given direction in the scattering vector (q) space and generate the two-dimensional scattering pattern on a given q plane. Several examples of the calculations are presented, demonstrating the method and its applicability. The presented results open new possibilities for the analysis of scattering patters obtained from oriented systems.

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“…For a more comprehensive review of SAXS theory we recommend several reviews . SAXS profiles are reported by intensity ( I ) as a function of momentum transfer vector ( q ).…”

Section: Introductionmentioning

confidence: 99%

“…For a more comprehensive review of SAXS theory we recommend several reviews. 8,9,[13][14][15][16] SAXS profiles are reported by intensity (I) as a function of momentum transfer vector (q). Large interatomic distances contribute to the intensity profile at small q, while short interatomic distances contribute to the intensity at large q.…”

Section: Introductionmentioning

confidence: 99%

BCL::SAXS: GPU accelerated Debye method for computation of small angle X-ray scattering profiles

et al. 2015

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Small angle X-ray scattering (SAXS) is an experimental technique used for structural characterization of macromolecules in solution. Here, we introduce BCL::SAXS – an algorithm designed to replicate SAXS profiles from rigid protein models at different levels of detail. We first show our derivation of BCL::SAXS and compare our results with the experimental scattering profile of Hen Egg White Lysozyme. Using this protein we show how to generate SAXS profiles representing: 1) complete models, 2) models with approximated side chain coordinates, and 3) models with approximated side chain and loop region coordinates. We evaluated the ability of SAXS profiles to identify a correct protein topology from a non-redundant benchmark set of proteins. We find that complete SAXS profiles can be used to identify the correct protein by receiver operating characteristic (ROC) analysis with an area under the curve (AUC) > 99%. We show how our approximation of loop coordinates between secondary structure elements improves protein recognition by SAXS for protein models without loop regions and side chains. Agreement with SAXS data is a necessary but not sufficient condition for structure determination. We conclude that experimental SAXS data can be used as a filter to exclude protein models with large structural differences from the native.

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Reconstruction of Saxs Profiles From Protein Structures

Cited by 38 publications

References 35 publications

A new definition and properties of the similarity value between two protein structures

A new definition and properties of the similarity value between two protein structures

Calculation of two-dimensional scattering patterns for oriented systems

BCL::SAXS: GPU accelerated Debye method for computation of small angle X-ray scattering profiles

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