Reduced representation of protein structure: implications on efficiency and scope of detection of structural similarity.

ABSTRACT:

Background

Computational comparison of two protein structures is the starting point of many methods that build on existing knowledge, such as structure modeling (including modeling of protein complexes and conformational changes), molecular replacement, or annotation by structural similarity. In a commonly used strategy, significant effort is invested in matching two sets of atoms. In a complementary approach, a global descriptor is assigned to the overall structure, thus losing track of the substructures within.

Results

Using a small set of geometric features, we define a reduced representation of protein structure, together with an optimizing function for matching two representations, to provide a pre-filtering stage in a database search. We show that, in a straightforward

SUBMITTER: Zhang ZH 

PROVIDER: S-EPMC3098053 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature