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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >PROTEIN SECONDARY STRUCTURE PREDICTION USING NMR CHEMICAL SHIFT DATA
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PROTEIN SECONDARY STRUCTURE PREDICTION USING NMR CHEMICAL SHIFT DATA

机译：利用NMR化学位移数据预测蛋白质二级结构。

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摘要

Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b) easily extendable to (the dynamic) new databases; and (c) approaching to the limit of accuracy. We introduce new approaches using k-nearest neighbor algorithm to do the basic prediction and use the BCJR algorithm to smooth the predictions and combine different predictions from chemical shifts and based on sequence information only. Our new system, SUCCES, improves the accuracy of all existing methods on a large dataset of 805 proteins (at 86% Q3 accuracy and at 92.6% accuracy when the boundary residues are ignored), and it is easily extendable to any new dataset without requiring any new training. The software is publicly available at http://monod.uwaterloo.camr/succes.
机译：根据化学位移信息准确确定蛋白质二级结构是NMR三级结构确定的关键步骤。相对而言，在此主题上的工作很少。需要对算法进行系统的研究，这些算法必须（a）对大型数据集具有鲁棒性； （b）易于扩展到（动态）新数据库； （c）接近准确性的极限。我们介绍了使用k最近邻算法进行基本预测的新方法，并使用BCJR算法对预测进行了平滑处理，并结合了仅基于序列信息的化学位移得出的不同预测。我们的新系统SUCCES可提高805种蛋白质的大型数据集的所有现有方法的准确性（Q3准确性为86％，忽略边界残基时的准确性为92.6％），并且可以轻松扩展到任何新数据集而无需任何新的培训。该软件可从http://monod.uwaterloo.camr/succes上公开获得。

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    YUZHONG ZHAO; BABAK ALIPANAHI; SHUAI CHENG LI; MING LI;

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    YUZHONG ZHAO The authors contributed equally to this work.Department of Computer Science, University of Science and Technology of China, Hefei, Anhui 230027, ChinaDavid R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON, N2L 3G1, Canadazyzh@mail.ustc.edu.cn BABAK ALIPANAHI The authors contributed equally to this work.David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON, N2L 3G1, Canada SHUAI CHENG LI David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON, N2L 3G1, Canada MING LI David R. Cheriton School of Computer Science, University of Waterloo, Waterloo, ON, N2L 3G1, Canadamli@uwaterloo.ca;

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    Protein structure prediction; NMR; chemical shift.;

    机译：蛋白质结构预测;NMR;化学位移。;

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