Andrzej Kolinski Research Group

Coarse-grained protein modeling

Modeling Software & Servers

Biomolecules — dynamics & interactions


ClusCo: clustering and comparison of protein models


BMC Bioinformatics, 14:62, 2013


BACKGROUND: The development, optimization and validation of protein modeling methods require efficient tools forstructural comparison. Frequently, a large number of models need to be compared with the targetnative 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 thebottlenecks in the protein modeling pipeline.

RESULTS: Clusco is fast and easy-to-use software for high-throughput comparison of protein models with dif-ferent 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 HierarchicalAgglomerative Clustering.

CONCLUSIONS: The application was highly optimized and written in C/C++, including the code for parallel execu-tion on CPU and GPU, which resulted in a significant speedup over similar clustering and scoringcomputation programs.