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|Title:||Computer prediction of allergen proteins from sequence-derived protein structural and physicochemical properties||Authors:||Cui, J.
Statistical learning method
Support vector machine
|Issue Date:||Jan-2007||Citation:||Cui, J., Han, L.Y., Li, H., Ung, C.Y., Tang, Z.Q., Zheng, C.J., Cao, Z.W., Chen, Y.Z. (2007-01). Computer prediction of allergen proteins from sequence-derived protein structural and physicochemical properties. Molecular Immunology 44 (4) : 514-520. ScholarBank@NUS Repository. https://doi.org/10.1016/j.molimm.2006.02.010||Abstract:||Background: Computational methods have been developed for predicting allergen proteins from sequence segments that show identity, homology, or motif match to a known allergen. These methods achieve good prediction accuracies, but are less effective for novel proteins with no similarity to any known allergen. Methods: This work tests the feasibility of using a statistical learning method, support vector machines, as such a method. The prediction system is trained and tested by using 1005 allergen proteins from the Allergome database and 22,469 non-allergen proteins from 7871 Pfam families. Results: Testing results by an independent set of 229 allergen and 6717 non-allergen proteins from 7871 Pfam families show that 93.0% and 99.9% of these are correctly predicted, which are comparable to the best results of other methods. Of the 18 novel allergen proteins non-homologous to any other proteins in the Swissprot database, 88.9% is correctly predicted. A further screening of 168,128 proteins in the Swissprot database finds that 2.9% of the proteins are predicted as allergen proteins, which is consistent with the estimated numbers from motif-based methods. Conclusions: Our study suggests that SVM is a potentially useful method for predicting allergen proteins and it has certain capability for predicting novel allergen proteins. Our software can be accessed at http://jing.cz3.nus.edu.sg/cgi-bin/APPEL. © 2006 Elsevier Ltd. All rights reserved.||Source Title:||Molecular Immunology||URI:||http://scholarbank.nus.edu.sg/handle/10635/105768||ISSN:||01615890||DOI:||10.1016/j.molimm.2006.02.010|
|Appears in Collections:||Staff Publications|
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