dc.contributor.author | Faraggi, Eshel | |
dc.contributor.author | Xue, Bin | |
dc.contributor.author | Zhou, Yaoqi | |
dc.date.accessioned | 2017-05-03T15:56:04Z | |
dc.date.available | 2017-05-03T15:56:04Z | |
dc.date.issued | 2009 | |
dc.date.modified | 2014-05-28T22:28:01Z | |
dc.identifier.issn | 0887-3585 | |
dc.identifier.doi | 10.1002/prot.22193 | |
dc.identifier.uri | http://hdl.handle.net/10072/57473 | |
dc.description.abstract | This article attempts to increase the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins through improved learning. Most methods developed for improving the back propagation algorithm of artificial neural networks are limited to small neural networks. Here, we introduce a guided-learning method suitable for networks of any size. The method employs a part of the weights for guiding and the other part for training and optimization. We demonstrate this technique by predicting residue solvent accessibility and real-value backbone torsion angles of proteins. In this application, the guiding factor is designed to satisfy the intuitive condition that for most residues, the contribution of a residue to the structural properties of another residue is smaller for greater separation in the protein-sequence distance between the two residues. We show that the guided-learning method makes a 2-4% reduction in 10-fold cross-validated mean absolute errors (MAE) for predicting residue solvent accessibility and backbone torsion angles, regardless of the size of database, the number of hidden layers and the size of input windows. This together with introduction of two-layer neural network with a bipolar activation function leads to a new method that has a MAE of 0.11 for residue solvent accessibility, 368 for w, and 228 for /. | |
dc.description.peerreviewed | Yes | |
dc.description.publicationstatus | Yes | |
dc.format.extent | 626083 bytes | |
dc.format.mimetype | application/pdf | |
dc.language | English | |
dc.language.iso | eng | |
dc.publisher | Wiley-Liss | |
dc.publisher.place | United States | |
dc.relation.ispartofstudentpublication | N | |
dc.relation.ispartofpagefrom | 847 | |
dc.relation.ispartofpageto | 856 | |
dc.relation.ispartofissue | 4 | |
dc.relation.ispartofjournal | Proteins: Structure, Function, and Bioinformatics | |
dc.relation.ispartofvolume | 74 | |
dc.rights.retention | Y | |
dc.subject.fieldofresearch | Mathematical sciences | |
dc.subject.fieldofresearch | Biological sciences | |
dc.subject.fieldofresearch | Information and computing sciences | |
dc.subject.fieldofresearchcode | 49 | |
dc.subject.fieldofresearchcode | 31 | |
dc.subject.fieldofresearchcode | 46 | |
dc.title | Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network | |
dc.type | Journal article | |
dc.type.description | C1 - Articles | |
dc.type.code | C - Journal Articles | |
gro.rights.copyright | © 2009 Wiley Periodicals, Inc. This is the accepted version of the following article: Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a two-layer neural network, Proteins: Structure, Function, and Bioinformatics, Vol. 74(4), 2009, pp. 847-856, which has been published in final form at dx.doi.org/10.1002/prot.22193. | |
gro.date.issued | 2009 | |
gro.hasfulltext | Full Text | |
gro.griffith.author | Zhou, Yaoqi | |