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rdf:type |
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lifeskim:mentions |
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pubmed:issue |
1
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pubmed:dateCreated |
2008-12-23
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pubmed:abstractText |
In this work, we aim to develop a computational approach for predicting DNA-binding sites in proteins from amino acid sequences. To avoid overfitting with this method, all available DNA-binding proteins from the Protein Data Bank (PDB) are used to construct the models. The random forest (RF) algorithm is used because it is fast and has robust performance for different parameter values. A novel hybrid feature is presented which incorporates evolutionary information of the amino acid sequence, secondary structure (SS) information and orthogonal binary vector (OBV) information which reflects the characteristics of 20 kinds of amino acids for two physical-chemical properties (dipoles and volumes of the side chains). The numbers of binding and non-binding residues in proteins are highly unbalanced, so a novel scheme is proposed to deal with the problem of imbalanced datasets by downsizing the majority class.
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pubmed:commentsCorrections |
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-10592235,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-11104519,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-1180967,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-11900253,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-12589754,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-14654694,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-14990443,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-15146487,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-15644130,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-16233974,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-16568445,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-16712732,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-16845003,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-16894602,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-17237068,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-17245807,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-17264128,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-17275170,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-17284455,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-17316627,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-17360525,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-17646316,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-17825469,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-2231712,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-9094735,
http://linkedlifedata.com/resource/pubmed/commentcorrection/19008251-9254694
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:chemical |
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pubmed:status |
MEDLINE
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pubmed:month |
Jan
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pubmed:issn |
1367-4811
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pubmed:author |
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pubmed:issnType |
Electronic
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pubmed:day |
1
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pubmed:volume |
25
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
30-5
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pubmed:dateRevised |
2009-11-18
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pubmed:meshHeading |
pubmed-meshheading:19008251-Algorithms,
pubmed-meshheading:19008251-Amino Acid Sequence,
pubmed-meshheading:19008251-Amino Acids,
pubmed-meshheading:19008251-Computational Biology,
pubmed-meshheading:19008251-DNA,
pubmed-meshheading:19008251-DNA-Binding Proteins,
pubmed-meshheading:19008251-Databases, Protein,
pubmed-meshheading:19008251-Models, Molecular,
pubmed-meshheading:19008251-Protein Binding,
pubmed-meshheading:19008251-ROC Curve
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pubmed:year |
2009
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pubmed:articleTitle |
Prediction of DNA-binding residues in proteins from amino acid sequences using a random forest model with a hybrid feature.
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pubmed:affiliation |
State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China.
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pubmed:publicationType |
Journal Article,
Research Support, Non-U.S. Gov't
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