Reconstruction of SAXS Profiles from Protein Structures

Daniel K Putnam; Edward W Lowe Jr; Jens Meiler

doi:10.5936/csbj.201308006

Reconstruction of SAXS Profiles from Protein Structures

Comput Struct Biotechnol J. 2013 Nov 26:8:e201308006. doi: 10.5936/csbj.201308006. eCollection 2013.

Authors

Daniel K Putnam¹, Edward W Lowe Jr², Jens Meiler³

Affiliations

¹ Center for Structural Biology ; Department of Biomedical Informatics.
² Center for Structural Biology ; Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA.
³ Center for Structural Biology ; Department of Biomedical Informatics ; Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA.

Abstract

Small angle X-ray scattering (SAXS) is used for low resolution structural characterization of proteins often in combination with other experimental techniques. After briefly reviewing the theory of SAXS we discuss computational methods based on 1) the Debye equation and 2) Spherical Harmonics to compute intensity profiles from a particular macromolecular structure. Further, we review how these formulas are parameterized for solvent density and hydration shell adjustment. Finally we introduce our solution to compute SAXS profiles utilizing GPU acceleration.

Keywords: AXES; CRYSOL; DALAI; Debye formula; FOXS; PHAISTOS; SASTBX; SAXSTER; small angle X-ray scattering; spherical harmonics.

Publication types

Review

Abstract

Publication types

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