DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale

被引：229

作者：

Zhou, Tianyin ^{[1
]}

Yang, Lin ^{[1
]}

Lu, Yan ^{[1
]}

Dror, Iris ^{[1
]}

Machado, Ana Carolina Dantas ^{[1
]}

Ghane, Tahereh ^{[1
]}

Di Felice, Rosa ^{[1
,2
]}

Rohs, Remo ^{[1
,2
,3
,4
,5
]}

机构：

[1] Univ So Calif, Dept Biol Sci, Mol & Computat Biol Program, Los Angeles, CA 90089 USA

[2] Univ So Calif, Dept Phys & Astron, Los Angeles, CA 90089 USA

[3] Univ So Calif, Dept Chem, Los Angeles, CA 90089 USA

[4] Univ So Calif, Dept Comp Sci, Los Angeles, CA 90089 USA

[5] Univ So Calif, Norris Comprehens Canc Ctr, Los Angeles, CA 90089 USA

来源：

NUCLEIC ACIDS RESEARCH | 2013年 / 41卷 / W1期

关键词：

MONTE-CARLO SIMULATIONS; MOLECULAR-DYNAMICS; MINOR-GROOVE; NUCLEIC-ACIDS; BINDING SPECIFICITY; FORCE-FIELD; SHAPE; RECOGNITION; PROTEINS; ORIGINS;

D O I：

10.1093/nar/gkt437

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We present a method and web server for predicting DNA structural features in a high-throughput (HT) manner for massive sequence data. This approach provides the framework for the integration of DNA sequence and shape analyses in genome-wide studies. The HT methodology uses a sliding-window approach to mine DNA structural information obtained from Monte Carlo simulations. It requires only nucleotide sequence as input and instantly predicts multiple structural features of DNA (minor groove width, roll, propeller twist and helix twist). The results of rigorous validations of the HT predictions based on DNA structures solved by X-ray crystallography and NMR spectroscopy, hydroxyl radical cleavage data, statistical analysis and cross-validation, and molecular dynamics simulations provide strong confidence in this approach. The DNAshape web server is freely available at http://rohslab.cmb.usc.edu/DNAshape/.

引用

页码：W56 / W62

页数：7

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