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学科主题: 物理化学
题名: A Structural-Based Strategy for Recognition of Transcription Factor Binding Sites
作者: Xu, Beisi1, 2, 3;  Schones, Dustin E.4;  Wang, Yongmei5;  Liang, Haojun6;  Li, Guohui1
通讯作者: 李国辉
刊名: PLOS ONE
发表日期: 2013-01-08
DOI: 10.1371/journal.pone.0052460
卷: 8, 期:1, 页:52460
收录类别: SCI
合作性质: 
文章类型: Article
部门归属: 11
项目归属: 1106
产权排名: 待补充
WOS标题词: Science & Technology
类目[WOS]: Multidisciplinary Sciences
资助者: 1,1
研究领域[WOS]: Science & Technology - Other Topics
英文摘要: Scanning through genomes for potential transcription factor binding sites (TFBSs) is becoming increasingly important in this post-genomic era. The position weight matrix (PWM) is the standard representation of TFBSs utilized when scanning through sequences for potential binding sites. However, many transcription factor (TF) motifs are short and highly degenerate, and methods utilizing PWMs to scan for sites are plagued by false positives. Furthermore, many important TFs do not have well-characterized PWMs, making identification of potential binding sites even more difficult. One approach to the identification of sites for these TFs has been to use the 3D structure of the TF to predict the DNA structure around the TF and then to generate a PWM from the predicted 3D complex structure. However, this approach is dependent on the similarity of the predicted structure to the native structure. We introduce here a novel approach to identify TFBSs utilizing structure information that can be applied to TFs without characterized PWMs, as long as a 3D complex structure (TF/DNA) exists. This approach utilizes an energy function that is uniquely trained on each structure. Our approach leads to increased prediction accuracy and robustness compared with those using a more general energy function. The software is freely available upon request.
关键词[WOS]: PROTEIN-DNA INTERACTIONS ;  STRUCTURE-BASED PREDICTION ;  SACCHAROMYCES-CEREVISIAE ;  ENERGY FUNCTION ;  ALL-ATOM ;  REGULATORY PROTEINS ;  TARGET SITES ;  SPECIFICITY ;  COMPLEXES ;  PROFILES
语种: 英语
原文出处: 查看原文
WOS记录号: WOS:000313429800015
Citation statistics: 
内容类型: 期刊论文
URI标识: http://cas-ir.dicp.ac.cn/handle/321008/119639
Appears in Collections:中国科学院大连化学物理研究所_期刊论文

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作者单位: 1.Chinese Acad Sci, Dalian Inst Chem Phys, State Key Lab Mol React Dynam, Lab Mol Modeling & Design, Dalian, Liaoning, Peoples R China
2.Univ Tennessee, Ctr Hlth Sci, Dept Microbiol Immunol & Biochem, Memphis, TN 38163 USA
3.Univ Tennessee, Ctr Hlth Sci, Ctr Integrat & Translat Gen, Memphis, TN 38163 USA
4.City Hope Natl Med Ctr, Beckman Res Inst, Dept Canc Biol, Duarte, CA 91010 USA
5.Univ Memphis, Dept Chem, Memphis, TN 38152 USA
6.Univ Sci & Technol China, Dept Polymer Sci & Engn, Hefei, Anhui, Peoples R China

Recommended Citation:
Xu, Beisi,Schones, Dustin E.,Wang, Yongmei,et al. A Structural-Based Strategy for Recognition of Transcription Factor Binding Sites[J]. PLOS ONE,2013,8(1):52460.
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