Improving protein template recognition by using small-angle x-ray scattering profiles.

ABSTRACT: Small-angle x-ray scattering (SAXS) is able to extract low-resolution protein shape information without requiring a specific crystal formation. However, it has found little use in atomic-level protein structure determination due to the uncertainty of residue-level structural assignment. We developed a new algorithm, SAXSTER, to couple the raw SAXS data with protein-fold-recognition algorithms and thus improve template-based protein-structure predictions. We designed nine different matching scoring functions of template and experimental SAXS profiles. The logarithm of the integrated correlation score showed the best template recognition ability and had the highest correlation with the true template modeling (TM)-score of the target structures. We tested the method in large-scale protein-fol

SUBMITTER: dos Reis MA 

PROVIDER: S-EPMC3297808 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature