Abstract
Motivation: Small angle X-ray scattering (SAXS) is an established method for studying biological macromolecules in solution, whereby the experimental scattering patterns relate to the quaternary and tertiary structure of the macromolecule. Here we present DARA, a web-server, that queries over 150 000 scattering profiles pre-computed from the high resolution models of macromolecules and biological assemblies in the Protein Data Bank, to rapidly find nearest neighbours of a given experimental or theoretical SAXS pattern. Identification of the best scattering equivalents provides a straightforward and automated way of structural assessment of macromolecules based on a SAXS profile. DARA results are useful e.g. for fold recognition and finding of biologically active oligomers.Availability and implementation: http://dara.embl-hamburg.de/Contact: svergun@embl-hamburg.de
Highlights
In a small angle X-ray scattering (SAXS) experiment a homogeneous solution of proteins, nucleic acids or their complexes is illuminated by a monochromatic X-ray beam
We present DARA, a web-server that rapidly compares over 150 000 scattering profiles pre-computed from models in the Protein Data Bank (PDB) (Berman et al, 2007) with a given SAXS pattern
2.1 Preparing the simulated SAXS data In DARA, all PDB entries are grouped into three categories: proteins, nucleic acids and protein:nucleic acid complexes
Summary
In a small angle X-ray scattering (SAXS) experiment a homogeneous solution of proteins, nucleic acids or their complexes is illuminated by a monochromatic X-ray beam. If an atomic model is available, its theoretical scattering can be computed and compared to the experimental data (Svergun et al, 1995). If one or several patterns agree with the experimental data the corresponding models may provide insights about the quaternary and sometimes tertiary structure. We present DARA, a web-server that rapidly compares over 150 000 scattering profiles pre-computed from models in the Protein Data Bank (PDB) (Berman et al, 2007) with a given SAXS pattern. The implementation features a new search algorithm combining principal component analysis and k-d trees for almost instantaneous (within a few seconds) identification of the scattering neighbours, includes nucleic acids and complexes in the search space, and provides an enhanced presentation of the results.
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