| 引用本文: | 邢龙生,李娟,方慧生,陈凯先.Profile-profile比对方法用于发现远距离同源模板[J].生物信息学,2013,11(1):16-21. |
| XING Long-sheng,LI Juan2,FANG Hui-sheng1,CHEN Kai-xian.Profile-profile alignment method for detection of distantly homologous template[J].Chinese Journal of Bioinformatics,2013,11(1):16-21. |
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| Profile-profile比对方法用于发现远距离同源模板 |
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邢龙生1, 李娟2, 方慧生1, 陈凯先3,4
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(1. 中国药科大学生命科学与技术学院,南京市 210009;;2. 南京市鼓楼医院血液科, 南京市 210008;;3. 中国科学院上海药物研究所药物发现与设计中心,上海市 201203;;4. 上海中医药大学,上海市 201203)
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| 摘要: |
| 基于模板的模建方法是蛋白质结构预测领域中最为准确有效的方法,该类方法的成功与否对模板质量的要求较高。为待预测序列找寻合适的模板,本文提出了一种profile-profile比对的方法将查询序列同模板库中的已知结构蛋白进行比对,然后根据比对结果的Z-score得分高低顺序挑选出合适的模板。结果表明:本文的profile-profile比对方法在测试集上的性能明显优于PSI-BLAST,相比PSI-BLAST在测试集上的准确度提高了约14.3%,配对t检验的结果表明准确度的提高具有统计显著性。从而得出如下结论:本文的profile-profile比对方法可以用于为序列相似性较低的待预测序列搜索远距离同源模板,并用于指导后续的三级结构预测。 |
| 关键词: profile-profile 比对,结构预测,远距离同源模板,PSI-BLAST |
| DOI：10.3969/j.issn.1672-5565.2013-01.20130103 |
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| Profile-profile alignment method for detection of distantly homologous template |
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XING Long-sheng1, LI Juan2, FANG Hui-sheng1, CHEN Kai-xian3,4
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(1. School of life science and technology, China Pharmaceutical University,Nanjing 210009,China; ;2. Hematology Department, Nanjing Drum Tower Hospital,Nanjing 210008,China; ;3. Drug Discovery and Design Center of Shanghai Instituteof Materia Medica, Chinese Academy of Sciences,Shanghai 201203,China; ;4. Shanghai University of Traditional Chinese Medicine,Shanghai 201203,China)
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| Abstract: |
| Template-based modeling was the most accurate and efficient method in the field of protein tertiary structure prediction, however, this Kind of method was highly dependent on the template quality. This article was aimed at establishing a kind of alignment method, which was used for detection of suitable templates for query sequence.A kind of profile-profile alignment method was proposed in this article, which firstly make alignments of query sequences and proteins with known structure in template library, followed the templates being selected out according to Z-score ranking of alignment results.The proposed profile-profile alignment method obviously outperformed PSI-BLAST on the testing sets. The accuracy was increased by 14.3% in comparison to PSI-BLAST on testing sets, which was statistically significant on a paired Students’ t test.The profile-profile alignment method in this article could be employed to identify distantly-related templates for query sequences with low sequence similarity, furthermore, the templates obtained from this method could be used to guide tertiary structure prediction of query sequence subsequently. |
| Key words: Profile-profile Alignment,Structure Prediction,Distantly Homologous Template PSI-BLAST |
