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Open AccessArticle

Graph-Based Community Detection for Decoy Selection in Template-Free Protein Structure Prediction

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Department of Computer Science, George Mason University, Fairfax, VA 22030, USA
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Department of Information Sciences and Technology, George Mason University, Fairfax, VA 22030, USA
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Department of Bioengineering, George Mason University, Fairfax, VA 22030, USA
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School of Systems Biology, George Mason University, Fairfax, VA 22030, USA
*
Author to whom correspondence should be addressed.
Current address: 4400 University Drive, MS 4A5, Fairfax, VA 22030, USA.
Molecules 2019, 24(5), 854; https://doi.org/10.3390/molecules24050854
Received: 13 January 2019 / Revised: 14 February 2019 / Accepted: 22 February 2019 / Published: 28 February 2019
Significant efforts in wet and dry laboratories are devoted to resolving molecular structures. In particular, computational methods can now compute thousands of tertiary structures that populate the structure space of a protein molecule of interest. These advances are now allowing us to turn our attention to analysis methodologies that are able to organize the computed structures in order to highlight functionally relevant structural states. In this paper, we propose a methodology that leverages community detection methods, designed originally to detect communities in social networks, to organize computationally probed protein structure spaces. We report a principled comparison of such methods along several metrics on proteins of diverse folds and lengths. We present a rigorous evaluation in the context of decoy selection in template-free protein structure prediction. The results make the case that network-based community detection methods warrant further investigation to advance analysis of protein structure spaces for automated selection of functionally relevant structures. View Full-Text
Keywords: protein structure space; nearest-neighbor graph; community detection; decoy selection; template-free protein structure prediction protein structure space; nearest-neighbor graph; community detection; decoy selection; template-free protein structure prediction
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MDPI and ACS Style

Kabir, K.L.; Hassan, L.; Rajabi, Z.; Akhter, N.; Shehu, A. Graph-Based Community Detection for Decoy Selection in Template-Free Protein Structure Prediction. Molecules 2019, 24, 854.

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