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Effects of the difference in similarity measures on the comparison of ligand-binding pockets using a reduced vector representation of pockets.

ABSTRACT: Comprehensive analysis and comparison of protein ligand-binding pockets are important to predict the ligands which bind to parts of putative ligand binding pockets. Because of the recent increase of protein structure information, such analysis demands a fast and efficient method for comparing ligand binding pockets. Previously we proposed a fast alignment-free method based on a simple representation of a ligand binding pocket with one 11-dimensional vector, which is suitable for such analysis. Based on that method, we conducted this study to expand and revise similarity measures of binding pockets and to investigate the effects of those modifications with two datasets for improving the ability to detect similar binding pockets. The new method exhibits higher detection performance of similar binding pockets than the previous methods and another existing accurate alignment-dependent method: APoc. Results also show that the effects of the modifications depend on the difficulty of the dataset, implying some avenues for methods of improvement.

SUBMITTER: Nakamura T

PROVIDER: S-EPMC5042158 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Effects of the difference in similarity measures on the comparison of ligand-binding pockets using a reduced vector representation of pockets.

Nakamura Tsukasa T Tomii Kentaro K

Biophysics and physicobiology 20160714

Comprehensive analysis and comparison of protein ligand-binding pockets are important to predict the ligands which bind to parts of putative ligand binding pockets. Because of the recent increase of protein structure information, such analysis demands a fast and efficient method for comparing ligand binding pockets. Previously we proposed a fast alignment-free method based on a simple representation of a ligand binding pocket with one 11-dimensional vector, which is suitable for such analysis. B ...[more]

PMID: 27924268

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Project description:BackgroundIn recent years, the important functional roles of RNAs in biological processes have been repeatedly demonstrated. Computing the similarity between two RNAs contributes to better understanding the functional relationship between them. But due to the long-range correlations of RNA, many efficient methods of detecting protein similarity do not work well. In order to comprehensively understand the RNA's function, the better similarity measure among RNAs should be designed to consider their structure features (base pairs). Current methods for RNA comparison could be generally classified into alignment-based and alignment-free.ResultsIn this paper, we propose a novel wavelet-based method based on RNA triple vector curve representation, named multi-scale RNA comparison. Firstly, we designed a novel numerical representation of RNA secondary structure termed as RNA triple vectors curve (TV-Curve). Secondly, we constructed a new similarity metric based on the wavelet decomposition of the TV-Curve of RNA. Finally we also applied our algorithm to the classification of non-coding RNA and RNA mutation analysis. Furthermore, we compared the results to the two well-known RNA comparison tools: RNAdistance and RNApdist. The results in this paper show the potentials of our method in RNA classification and RNA mutation analysis.ConclusionWe provide a better visualization and analysis tool named TV-Curve of RNA, especially for long RNA, which can characterize both sequence and structure features. Additionally, based on TV-Curve representation of RNAs, a multi-scale similarity measure for RNA comparison is proposed, which can capture the local and global difference between the information of sequence and structure of RNAs. Compared with the well-known RNA comparison approaches, the proposed method is validated to be outstanding and effective in terms of non-coding RNA classification and RNA mutation analysis. From the numerical experiments, our proposed method can capture more efficient and subtle relationship of RNAs.

Dataset Information

Effects of the difference in similarity measures on the comparison of ligand-binding pockets using a reduced vector representation of pockets.

Publications

Effects of the difference in similarity measures on the comparison of ligand-binding pockets using a reduced vector representation of pockets.

Similar Datasets

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