Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues.

ABSTRACT:

Background

The emergence of structural genomics presents significant challenges in the annotation of biologically uncharacterized proteins. Unfortunately, our ability to analyze these proteins is restricted by the limited catalog of known molecular functions and their associated 3D motifs.

Results

In order to identify novel 3D motifs that may be associated with molecular functions, we employ an unsupervised, two-phase clustering approach that combines k-means and hierarchical clustering with knowledge-informed cluster selection and annotation methods. We applied the approach to approximately 20,000 cysteine-based protein microenvironments (3D regions 7.5 A in radius) and identified 70 interesting clusters, some of which represent known motifs (e.g. metal binding and phosphat

SUBMITTER: Wu S 

PROVIDER: S-EPMC2833161 | biostudies-literature | 2010 Feb

REPOSITORIES: biostudies-literature