Protein functional surfaces: global shape matching and local spatial alignments of ligand binding sites.

ABSTRACT:

Background

Protein surfaces comprise only a fraction of the total residues but are the most conserved functional features of proteins. Surfaces performing identical functions are found in proteins absent of any sequence or fold similarity. While biochemical activity can be attributed to a few key residues, the broader surrounding environment plays an equally important role.

Results

We describe a methodology that attempts to optimize two components, global shape and local physicochemical texture, for evaluating the similarity between a pair of surfaces. Surface shape similarity is assessed using a three-dimensional object recognition algorithm and physicochemical texture similarity is assessed through a spatial alignment of conserved residues between the surfaces. The compari

SUBMITTER: Binkowski TA 

PROVIDER: S-EPMC2626596 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature