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QuaBingo: Quaternary Structure Prediction by the Composition of Block and Functional Domain for Oligomeric Proteins
Protein quaternary structure classification
functional domain composition
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|摘要:||蛋白質四級結構與基因調控和訊號傳遞等許多生物功能有緊密相關性，使得蛋白質具有形態機能多樣性，能執行變構效應及更複雜的功能。本研究提出block composition特徵編碼方法，以保留性motif序列區塊為基礎，不僅包含了保留性殘基的特定序列模式，而且包含功能和結構組成訊息，有助於發掘隱藏的蛋白質聚合機制；同時再結合functional domain composition資訊，發展出「QuaBingo」預測同源和異源寡聚體四級結構類型。QuaBingo由三層分類器建構而成。第一層使用SVM作為分類器，根據蛋白質序列中的區塊、功能域組成進行特徵編碼。為了改善第一層的方法，使用第二層SVM整合第一層的輸出結果，然後送入第三層由random forest所建立的分類器中，決定蛋白質所屬之17種四級結構類型。十倍交叉驗證結果顯示， block composition之單體、同源和異源寡聚體整體準確率優於functional domain composition和solvent accessibility之胺基酸組成方法。特徵方法的整合結果，大部分的類別獲得1%~6%的提升。在功能性分析的部份，QuaBingo對於酵素、基因調控、訊息傳遞等蛋白質擁有較佳的預測能力。|
Quaternary structures of proteins are closely relevant to gene regulation, signal transduction and many other biological functions of proteins. Protein oligomers are usually with symmetry and morphological diversity can perform allosteric effects and more complex functions. In this study, a method based on protein conserved motif composition in blocks format for feature extraction was proposed. The method is called block composition which contains not only information of specific sequence patterns but also function and structural features, it is useful to explore the hidden mechanisms of protein aggregation. In this paper, we developed the quaternary structure attribute prediction system called "QuaBingo" which also combined with functional domain composition information. QuaBingo constructed by three-layer classifiers that can identify monomer, homo- and hetero-oligomer quaternary structure. The building of first layer classifiers using SVM based on blocks and functional domains of proteins. In order to improve the performance of the first layer, thus the second layer SVM was used to process the outputs of the first layer. Finally, the results were determined by random forest of the third layer. 10-fold cross-validation results show that the block composition obtains better results for monomer, homo- and hetero-oligomers than functional domain composition and the pseudo amino acid composition method based on solvent accessibility. Additionally, results of the integration method of characteristics that indicates the accuracy of most quaternary structure classifications reached between 1% and 6% improvement. In functional analysis, QuaBingo has better predictive ability for enzymes, gene regulation and signal transduction, might be useful for related protein research.
|Appears in Collections:||生物科技學研究所|
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