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

• Published in: Proteins, structure, function, and bioinformatics Vol. 83; no. 8; pp. 1500 - 1512
• Main Authors: Putnam, Daniel K., Weiner, Brian E., Woetzel, Nils, Lowe Jr, Edward W., Meiler, Jens
• Format: Journal Article
• Language: English
• Published: United States Blackwell Publishing Ltd 01.08.2015; Wiley Subscription Services, Inc; Wiley
• Subjects: Algorithms; BASIC BIOLOGICAL SCIENCES; Crystal structure; Debye formula; GPU acceleration; Humans; Models, Molecular; Proteins; Proteins - chemistry; ROC Curve; SAXS; Scattering, Small Angle; Topology; X-Ray Diffraction - methods; Debye formula; proteins; GPU acceleration; SAXS
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.24838

ABSTRACT 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 SAχS 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. Proteins 2015; 83:1500–1512. © 2015 Wiley Periodicals, Inc.