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- W2575992743 abstract "The interaction between proteins and DNA play important roles in numerous biological processes. Researchers have been trying to explain how protein-DNA interactions achieve their desired binding affinity and specificity using various methods ranging from molecular and genetic experiments to computational methods. In this work, we present an innovative graph method for the discovery of structure patterns that are favored in the protein-DNA interfaces. We evaluated the biological significance of the patterns discovered by the proposed method using three independent experiments. The first one showed that the patterns could be used to discriminate DNA-binding sites versus non-DNA-binding sites with 79.1% accuracy, 88.3% specificity, and 69.8% sensitivity. In the second experiment, we compared the patterns with expert annotations in the UniProtKB, a comprehensive database of protein function information. The comparison showed that the patterns had a significant overlap with amino acid residues that have been proven to be crucial for DNA-binding in biological experiments like mutagenesis. In the third test, we used the patterns to build a simple scoring function for protein-DNA docking. The scoring function assigned score to a docking pose based on the number of patterns found on the protein-DNA interface of the pose. Despite its simplicity, the scoring method achieved slightly better performance than FTdock, a well-established scoring method that took into consideration shape complementarity, electrostatics, and biochemical information. These results confirmed the significance of the discovered patterns. The proposed graph method will be a very helpful tool for studying the protein-DNA interaction and other type of molecular interactions." @default.
- W2575992743 created "2017-01-26" @default.
- W2575992743 creator A5021167284 @default.
- W2575992743 creator A5059801255 @default.
- W2575992743 date "2016-12-01" @default.
- W2575992743 modified "2023-09-24" @default.
- W2575992743 title "Mining structure patterns on the protein-DNA interfaces" @default.
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- W2575992743 doi "https://doi.org/10.1109/bibm.2016.7822780" @default.
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