Source:http://linkedlifedata.com/resource/pubmed/id/19508202
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| Predicate | Object |
|---|---|
| rdf:type | |
| lifeskim:mentions | |
| pubmed:issue |
3
|
| pubmed:dateCreated |
2010-3-23
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| pubmed:abstractText |
The interactions between RNA-binding proteins (RBPs) with RNA play key roles in managing some of the cell's basic functions. The identification and prediction of RNA binding sites is important for understanding the RNA-binding mechanism. Computational approaches are being developed to predict RNA-binding residues based on the sequence- or structure-derived features. To achieve higher prediction accuracy, improvements on current prediction methods are necessary. We identified that the structural neighbors of RNA-binding and non-RNA-binding residues have different amino acid compositions. Combining this structure-derived feature with evolutionary (PSSM) and other structural information (secondary structure and solvent accessibility) significantly improves the predictions over existing methods. Using a multiple linear regression approach and 6-fold cross validation, our best model can achieve an overall correct rate of 87.8% and MCC of 0.47, with a specificity of 93.4%, correctly predict 52.4% of the RNA-binding residues for a dataset containing 107 non-homologous RNA-binding proteins. Compared with existing methods, including the amino acid compositions of structure neighbors lead to clearly improvement. A web server was developed for predicting RNA binding residues in a protein sequence (or structure),which is available at http://mcgill.3322.org/RNA/.
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| pubmed:language |
eng
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| pubmed:journal | |
| pubmed:citationSubset |
IM
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| pubmed:chemical | |
| pubmed:status |
MEDLINE
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| pubmed:month |
Mar
|
| pubmed:issn |
1875-5305
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| pubmed:author | |
| pubmed:issnType |
Electronic
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| pubmed:volume |
17
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| pubmed:owner |
NLM
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| pubmed:authorsComplete |
Y
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| pubmed:pagination |
287-96
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| pubmed:meshHeading |
pubmed-meshheading:19508202-Databases, Protein,
pubmed-meshheading:19508202-Linear Models,
pubmed-meshheading:19508202-Protein Binding,
pubmed-meshheading:19508202-Protein Interaction Domains and Motifs,
pubmed-meshheading:19508202-Proteomics,
pubmed-meshheading:19508202-RNA-Binding Proteins,
pubmed-meshheading:19508202-ROC Curve,
pubmed-meshheading:19508202-Reproducibility of Results,
pubmed-meshheading:19508202-Sequence Analysis, Protein
|
| pubmed:year |
2010
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| pubmed:articleTitle |
Improve the prediction of RNA-binding residues using structural neighbours.
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| pubmed:affiliation |
School of Life Sciences, Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China (USTC), Hefei, Anhui, 230027, China. jeele@mail.ustc.edu.cn
|
| pubmed:publicationType |
Journal Article,
Research Support, Non-U.S. Gov't
|