运用PDB中的同源信息提高NetTurnP的蛋白质β转角预测精度
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湖南省杰出青年科学基金(10JJ1005)和高等学校博士点基金(200805370002)资助项目


Using Homology Information From PDB to Improve The Accuracy of Protein β-turn Prediction by NetTurnP
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This work was supported by grants from The Science Foundation for Distinguished Young Scholars of Hunan Province, China (10JJ1005), The Research Fund for The Doctoral Program of Higher Education of China (200805370002)

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    摘要:

    β转角作为一种蛋白质二级结构类型在蛋白质折叠、蛋白质稳定性、分子识别等方面具有重要作用.现有的β转角预测方法,没有将PDB等结构数据库中先前存在的同源序列的结构信息映射到待预测的蛋白质序列上.PDB存储的结构已超过70 000,因此对一条新确定的序列,有较大可能性从PDB中找到其同源序列.本文融合PDB中提取的同源结构信息(对每一待测序列,仅使用先于该序列存储于PDB中的同源信息)与NetTurnP预测,提出了一种新的β转角预测方法BTMapping,在经典的BT426数据集和本文构建的数据集EVA937上,以马修斯相关系数表示的预测精度分别为0.56、0.52,而仅使用NetTurnP的为0.50、0.46,以Qtotal表示的预测精度分别为81.4%、80.4%,而仅使用NetTurnP的为78.2%、77.3%.结果证实同源结构信息结合先进的β转角预测器如NetTurnP有助于改进β转角识别.BTMapping程序及相关数据集可从http://www.bio530.weebly.com获得.

    Abstract:

    β-Turn is a secondary protein structure type that is important in protein folding, protein stability and molecular recognition processes. To date, various methods have been put forward to predict β-turns, but none of them have tried directly to map the structures of pre-existing homologues from structural databases like RCSB PDB to the protein to be predicted. Given the large size of PDB (>70 000 structures), it is actually of high possibility to find a structural homologue for a newly identified sequence. In this work, we present a new method that predicts β-turns by combining homology information extracted from PDB with the results predicted by NetTurnP. Two datasets, the golden set BT426 and the self-constructed dataset EVA937, are used to assess our method. For each sequence in both datasets, only homologues deposited earlier than the sequence in PDB are employed. We have achieved Matthews correlation coefficients (MCCs) of 0.56, 0.52 respectively, which are higher than those obtained by NetTurnP alone of 0.50, 0.46, and the prediction accuracies (Qtotal) obtained using our method are 81.4% and 80.4% separately, while NetTurnP alone achieves 78.2% and 77.3%. The results confirm that combining the homology information with state-of-the-art β-turn predictors like NetTurnP can significantly improve the prediction accuracy. A Java program called BTMapping has been written to implement our method, which is freely available at http://www.bio530.weebly.com together with the related datasets.

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钱刚,王海燕,袁哲明.运用PDB中的同源信息提高NetTurnP的蛋白质β转角预测精度[J].生物化学与生物物理进展,2012,39(5):472-482

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历史
  • 收稿日期:2011-08-11
  • 最后修改日期:2011-10-25
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  • 在线发布日期: 2011-11-14
  • 出版日期: 2012-05-20