Unknown

Dataset Information

0

ClusCo: clustering and comparison of protein models.


ABSTRACT: BACKGROUND: The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to be compared with the target native structure. The main reason for the development of Clusco software was to create a high-throughput tool for all-versus-all comparison, because calculating similarity matrix is the one of the bottlenecks in the protein modeling pipeline. RESULTS: Clusco is fast and easy-to-use software for high-throughput comparison of protein models with different similarity measures (cRMSD, dRMSD, GDT_TS, TM-Score, MaxSub, Contact Map Overlap) and clustering of the comparison results with standard methods: K-means Clustering or Hierarchical Agglomerative Clustering. CONCLUSIONS: The application was highly optimized and written in C/C++, including the code for parallel execution on CPU and GPU, which resulted in a significant speedup over similar clustering and scoring computation programs.

SUBMITTER: Jamroz M 

PROVIDER: S-EPMC3645956 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

altmetric image

Publications

ClusCo: clustering and comparison of protein models.

Jamroz Michal M   Kolinski Andrzej A  

BMC bioinformatics 20130222


<h4>Background</h4>The development, optimization and validation of protein modeling methods require efficient tools for structural comparison. Frequently, a large number of models need to be compared with the target native structure. The main reason for the development of Clusco software was to create a high-throughput tool for all-versus-all comparison, because calculating similarity matrix is the one of the bottlenecks in the protein modeling pipeline.<h4>Results</h4>Clusco is fast and easy-to  ...[more]

Similar Datasets

| S-EPMC3403935 | biostudies-literature
| S-EPMC5112798 | biostudies-literature
| S-EPMC6329467 | biostudies-literature
| S-EPMC6338433 | biostudies-literature
| S-EPMC1925120 | biostudies-other
| S-EPMC3941951 | biostudies-literature
| S-EPMC3382433 | biostudies-literature
| S-EPMC6561975 | biostudies-literature
| S-EPMC3065697 | biostudies-literature
| S-EPMC7549635 | biostudies-literature