A new size-independent score for pairwise protein structure alignment and its application to structure classification and nucleic-acid binding prediction.

ABSTRACT: A structure alignment program aligns two structures by optimizing a scoring function that measures structural similarity. It is highly desirable that such scoring function is independent of the sizes of proteins in comparison so that the significance of alignment across different sizes of the protein regions aligned is comparable. Here, we developed a new score called SP-score that fixes the cutoff distance at 4 Å and removed the size dependence using a normalization prefactor. We further built a program called SPalign that optimizes SP-score for structure alignment. SPalign was applied to recognize proteins within the same structure fold and having the same function of DNA or RNA binding. For fold discrimination, SPalign improves sensitivity over TMalign for the chain-level comparison by

SUBMITTER: Yang Y 

PROVIDER: S-EPMC3393833 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature