Fast structure similarity searches among protein models: efficient clustering of protein fragments.

ABSTRACT:

Background

For many predictive applications a large number of models is generated and later clustered in subsets based on structure similarity. In most clustering algorithms an all-vs-all root mean square deviation (RMSD) comparison is performed. Most of the time is typically spent on comparison of non-similar structures. For sets with more than, say, 10,000 models this procedure is very time-consuming and alternative faster algorithms, restricting comparisons only to most similar structures would be useful.

Results

We exploit the inverse triangle inequality on the RMSD between two structures given the RMSDs with a third structure. The lower bound on RMSD may be used, when restricting the search of similarity to a reasonably low RMSD threshold value, to speed up similarity s

SUBMITTER: Fogolari F 

PROVIDER: S-EPMC3403935 | biostudies-literature | 2012 May

REPOSITORIES: biostudies-literature