Using Situs for the registration of protein structures with low-resolutionbead models from X-ray solution scattering

Three-dimensional bead models of proteins in solution are routinely determi ned from one-dimensional small-angle X-ray scattering (SAXS) data. The Situ s software provides a novel set of visualization and registration procedure s to facilitate the localization of protein structures in low-resolution SA XS bead models. The docking algorithm takes advantage of a reduced represen tation of the input data sets by means of topology-representing neural netw orks to expedite the rigid-body search. The precision of the docking was te sted on ten different simulated bead models: for >100 beads typically arisi ng in SAXS models, a docking precision of the order of an (a) over circle n gstr(o)double over dotm can be achieved. The shape-matching score captured the correct solutions in all ten trial cases and was sufficiently stringent to yield unique matches in seven systems. A size-invariant shape descripto r of 'sphericity' is proposed to assess the onset of ambiguity in the match ing of globular molecules. The software, a tutorial and supplementary data are available at http://situs.scripps.edu/saxs.