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Open Access Highly Accessed Methodology article

An improved method to detect correct protein folds using partial clustering

Jianjun Zhou1 and David S Wishart2*

Author Affiliations

1 JHK Co., Ltd., 2049 Heping Road, Shenzhen, Guangdong, 518010, China

2 Departments of Computing Science and Biological Sciences, 2–21 Athabasca Hall, University of Alberta, Edmonton, Alberta, T6G 2E8, Canada

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BMC Bioinformatics 2013, 14:11  doi:10.1186/1471-2105-14-11

Published: 16 January 2013



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.


We propose a new scheme that performs rapid but incomplete clustering on protein decoys. Our method detects structurally similar decoys (measured using either Cα RMSD or GDT-TS score) and extracts representatives from them without assigning every decoy to a cluster. We integrated our new clustering strategy with several different scoring functions to assess both the performance and speed in identifying correct or near-correct folds. Experimental results on 35 Rosetta decoy sets and 40 I-TASSER decoy sets show that our method can improve the correct fold detection rate as assessed by two different quality criteria. This improvement is significantly better than two recently published clustering methods, Durandal and Calibur-lite. Speed and efficiency testing shows that our method can handle much larger decoy sets and is up to 22 times faster than Durandal and Calibur-lite.


The new method, named HS-Forest, avoids the computationally expensive task of clustering every decoy, yet still allows superior correct-fold selection. Its improved speed, efficiency and decoy-selection performance should enable structure prediction researchers to work with larger decoy sets and significantly improve their ab initio structure prediction performance.