An improved method to detect correct protein folds using partial clustering.

ABSTRACT:

Background

Structure-based clustering is commonly used to identify correct protein folds among candidate folds (also called decoys) generated by protein structure prediction programs. However, traditional clustering methods exhibit a poor runtime performance on large decoy sets. We hypothesized that a more efficient "partial" clustering approach in combination with an improved scoring scheme could significantly improve both the speed and performance of existing candidate selection methods.

Results

We propose a new scheme that performs rapid but incomplete clustering on protein decoys. Our method detects structurally similar decoys (measured using either C(α) RMSD or GDT-TS score) and extracts representatives from them without assigning every decoy to a cluster. We integrated

SUBMITTER: Zhou J 

PROVIDER: S-EPMC3626854 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature