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Open AccessArticle

Selecting Near-Native Protein Structures from Predicted Decoy Sets Using Ordered Graphlet Degree Similarity

School of Information Science and Engineering, Lanzhou University, Lanzhou 730000, China
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Author to whom correspondence should be addressed.
Genes 2019, 10(2), 132; https://doi.org/10.3390/genes10020132
Received: 28 November 2018 / Revised: 3 February 2019 / Accepted: 4 February 2019 / Published: 11 February 2019
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Abstract

Effective prediction of protein tertiary structure from sequence is an important and challenging problem in computational structural biology. Ab initio protein structure prediction is based on amino acid sequence alone, thus, it has a wide application area. With the ab initio method, a large number of candidate protein structures called decoy set can be predicted, however, it is a difficult problem to select a good near-native structure from the predicted decoy set. In this work we propose a new method for selecting the near-native structure from the decoy set based on both contact map overlap (CMO) and graphlets. By generalizing graphlets to ordered graphs, and using a dynamic programming to select the optimal alignment with an introduced gap penalty, a GR_score is defined for calculating the similarity between the three-dimensional (3D) decoy structures. The proposed method was applied to all 54 single-domain targets in CASP11 and all 43 targets in CASP10, and ensemble clustering was used to cluster the protein decoy structures based on the computed CR_scores. The most popular centroid structure was selected as the near-native structure. The experiments showed that compared to the SPICKER method, which is used in I-TASSER, the proposed method can usually select better near-native structures in terms of the similarity between the selected structure and the true native structure. View Full-Text
Keywords: GR_score; dynamic programming; gap penalty; near-native protein; protein structure prediction GR_score; dynamic programming; gap penalty; near-native protein; protein structure prediction
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Han, X.; Li, L.; Lu, Y. Selecting Near-Native Protein Structures from Predicted Decoy Sets Using Ordered Graphlet Degree Similarity. Genes 2019, 10, 132.

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