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. 2013 Feb 22:14:62.
doi: 10.1186/1471-2105-14-62.

ClusCo: clustering and comparison of protein models

Michal Jamroz  1 , Andrzej Kolinski
Affiliations

ClusCo: clustering and comparison of protein models

Michal Jamroz et al. BMC Bioinformatics. .

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.

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Figures

Figure 1
Figure 1
Comparison of running time of all-versus-all Clusco and qcprot. cRMSD computation for three proteins of different length (71, 215 and 887 residues). For N models it compute N(N−1)/2 cRMSD values.
See this image and copyright information in PMC

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