20089514

Source:http://linkedlifedata.com/resource/pubmed/id/20089514

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Predicate	Object
rdf:type	pubmed:Citation
lifeskim:mentions	umls-concept:C0012940, umls-concept:C0020792, umls-concept:C0332875, umls-concept:C0679792, umls-concept:C1705194
pubmed:issue	5
pubmed:dateCreated	2010-2-25
pubmed:abstractText	SUMMARY: The iDBPs server uses the three-dimensional (3D) structure of a query protein to predict whether it binds DNA. First, the algorithm predicts the functional region of the protein based on its evolutionary profile; the assumption is that large clusters of conserved residues are good markers of functional regions. Next, various characteristics of the predicted functional region as well as global features of the protein are calculated, such as the average surface electrostatic potential, the dipole moment and cluster-based amino acid conservation patterns. Finally, a random forests classifier is used to predict whether the query protein is likely to bind DNA and to estimate the prediction confidence. We have trained and tested the classifier on various datasets and shown that it outperformed related methods. On a dataset that reflects the fraction of DNA binding proteins (DBPs) in a proteome, the area under the ROC curve was 0.90. The application of the server to an updated version of the N-Func database, which contains proteins of unknown function with solved 3D-structure, suggested new putative DBPs for experimental studies. AVAILABILITY: http://idbps.tau.ac.il/
pubmed:commentsCorrections	http://linkedlifedata.com/resource/pubmed/commentcorrection/20089514-12589754, http://linkedlifedata.com/resource/pubmed/commentcorrection/20089514-15201400, http://linkedlifedata.com/resource/pubmed/commentcorrection/20089514-15312763, http://linkedlifedata.com/resource/pubmed/commentcorrection/20089514-15356290, http://linkedlifedata.com/resource/pubmed/commentcorrection/20089514-15608167, http://linkedlifedata.com/resource/pubmed/commentcorrection/20089514-16284202, http://linkedlifedata.com/resource/pubmed/commentcorrection/20089514-16551468, http://linkedlifedata.com/resource/pubmed/commentcorrection/20089514-18515839, http://linkedlifedata.com/resource/pubmed/commentcorrection/20089514-18971256, http://linkedlifedata.com/resource/pubmed/commentcorrection/20089514-19081051, http://linkedlifedata.com/resource/pubmed/commentcorrection/20089514-19233205
pubmed:language	eng
pubmed:journal	http://linkedlifedata.com/resource/pubmed/journal/9808944
pubmed:citationSubset	IM
pubmed:chemical	http://linkedlifedata.com/resource/pubmed/chemical/DNA-Binding Proteins
pubmed:status	MEDLINE
pubmed:month	Mar
pubmed:issn	1367-4811
pubmed:author	pubmed-author:Ben-TalNirN, pubmed-author:LeslieChristinaC, pubmed-author:NimrodGuyG, pubmed-author:SchushanMayaM, pubmed-author:SzilágyiAndrásA
pubmed:issnType	Electronic
pubmed:day	1
pubmed:volume	26
pubmed:owner	NLM
pubmed:authorsComplete	Y
pubmed:pagination	692-3
pubmed:dateRevised	2010-9-28
pubmed:meshHeading	pubmed-meshheading:20089514-Binding Sites, pubmed-meshheading:20089514-DNA-Binding Proteins, pubmed-meshheading:20089514-Databases, Protein, pubmed-meshheading:20089514-Internet, pubmed-meshheading:20089514-Sequence Analysis, Protein, pubmed-meshheading:20089514-Software
pubmed:year	2010
pubmed:articleTitle	iDBPs: a web server for the identification of DNA binding proteins.
pubmed:affiliation	Department of Biochemistry, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel.
pubmed:publicationType	Journal Article, Research Support, Non-U.S. Gov't