Detecting sequence and structure homology via an integrative kernel: A case-study in recognizing enzymes

机译：通过整合核检测序列和结构同源性：识别酶的案例研究

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Sequence and structure are complementary pieces of information that can be used to infer protein function. We study and compare sequence, structure and sequence-structure integrative kernels to recognize proteins with enzymatic function. Using a support-vector machine, we show that kernels that combine sequence and structure information typically perform better (AUC 0.73) at this task than kernels that exploit either type of information exclusively. We find that the feature space of structure kernels complements that of sequence kernels, making both sources of similarity more accessible to kernel methods.

机译：序列和结构是可以用来推断蛋白质功能的互补信息。我们研究和比较序列，结构和序列结构整合核，以识别具有酶促功能的蛋白质。使用支持向量机，我们证明了结合序列和结构信息的内核在此任务上的性能通常比专门利用这两种信息的内核更好（AUC 0.73）。我们发现，结构核的特征空间补充了序列核的特征空间，使两种相似性来源更易于内核方法访问。

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《Computational Intelligence in Bioinformatics and Computational Biology, 2009. CIBCB '09》|2009年|46-52|共7页
会议地点 Nashville TN(US);Nashville TN(US)
作者
Arieshanti I.; Boden M.; Maetschke S.; Buske F.A.;
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Inst. for Mol. Biosci., Univ. of Queensland, Brisbane, QLD;

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enzymes; molecular biophysics; integrative kernel; protein function; sequence detection; structure homology detection;

机译：酶;分子生物物理学;整合核;蛋白质功能;序列检测;结构同源性检测;

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1. Detecting subtle functional differences in ketopantoate reductase and related enzymes using a rule-based approach with sequence-structure homology recognition scores [J] . MondalS., NagaoC., MizuguchiK. Protein engineering design & selection: PEDS . 2010,第11a12期

机译：使用具有序列结构同源性识别评分的基于规则的方法，检测酮戊酸酯还原酶和相关酶中的细微功能差异
2. Detecting subtle functional differences in ketopantoate reductase and related enzymes using a rule-based approach with sequence-structuren homology recognition scores [J] . Kenji Mizuguchi Protein Engineering, Design and Selection . 2010,第11期

机译：使用基于规则的，具有序列结构同源性识别评分的方法，检测酮戊酸酯还原酶和相关酶中的细微功能差异
3. Sequence analysis of the NgoPII methyltransferase gene from Neisseria gonorrhoeae P9: homologies with other enzymes recognizing the sequence 5′-GGCC-3′ [J] . Jon R. Saunders, Kevin M. Sullivan Nucleic acids research . 1988,第10期

机译：淋病奈瑟氏球菌P9的NgoPII甲基转移酶基因的序列分析：与识别序列5'-GGCC-3'的其他酶同源
4. Detecting Sequence and Structure Homology via an Integrative Kernel: A Case-Study in Recognizing Enzymes [C] . Isye Arieshanti, Mikael Boden, Stefan Maetschke, IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology . 2009

机译：通过整合核检测序列和结构同源性：识别酶的案例研究
5. Detecting cis-regulatory modules by modeling correlated structures in genomic sequences. [D] . Zhou, Qing. 2006

机译：通过对基因组序列中的相关结构进行建模来检测顺式调控模块。
6. Sequence analysis of the NgoPII methyltransferase gene from Neisseria gonorrhoeae P9: homologies with other enzymes recognizing the sequence 5-GGCC-3. [O] . K M Sullivan, J R Saunders 1988

机译：淋病奈瑟氏球菌P9的NgoPII甲基转移酶基因的序列分析：与识别序列5-GGCC-3的其他酶同源。
7. Detecting subtle functional differences in ketopantoate reductase and related enzymes using a rule-based approach with sequence-structure homology recognition scores [O] . S. Mondal, C. Nagao, K. Mizuguchi 2010

机译：利用基于规则的方法检测酮丙酯还原酶和相关酶的微妙功能差异，序列结构同源性同源性同源识别分数
8. Integration of Structural and Sequence Information for Homology-Based Modeling of Proteins [R] . Gribskov, M. 2003

机译：基于同源性的蛋白质建模的结构和序列信息的整合

Detecting sequence and structure homology via an integrative kernel: A case-study in recognizing enzymes

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