by Michael Fernández, Leyden Fernández, José Abreu, Miguel Garriga
Abstract:
Voltage-gated K+ ion channels (VKCs) are membrane proteins that regulate the passage of potassium ions through membranes. This work reports a classification scheme of VKCs according to the signs of three electrophysiological variables: activation threshold voltage (Vt), half-activation voltage (Va50) and half-inactivation voltage (Vh50). A novel 3D pseudo-folding graph representation of protein sequences encoded the VKC sequences. Amino acid pseudo-folding 3D distances count (AAp3DC) descriptors, calculated from the Euclidean distances matrices (EDMs) were tested for building the classifiers. Genetic algorithm (GA)-optimized support vector machines (SVMs) with a radial basis function (RBF) kernel well discriminated between VKCs having negative and positive/zero Vt, Va50 and Vh50 values with overall accuracies about 80, 90 and 86%, respectively, in crossvalidation test. We found contributions of the “pseudo-core” and “pseudo-surface” of the 3D pseudo-folded proteins to the discrimination between VKCs according to the three electrophysiological variables. © 2008 Elsevier Inc. All rights reserved.
Reference:
Classification of voltage-gated K+ ion channels from 3D pseudo-folding graph representation of protein sequences using genetic algorithm-optimized support vector machines (Michael Fernández, Leyden Fernández, José Abreu, Miguel Garriga), In Journal of Molecular Graphics and Modelling, volume 26, 2008. (http://www.scopus.com/inward/record.url?eid=2-s2.0-42749090642&partnerID=40&md5=01486f23c594fede840361bf77db5e8a http://www.ncbi.nlm.nih.gov/pubmed/18289899) (cited By (since 1996) 3)
Bibtex Entry:
Title = {Classification of voltage-gated K+ ion channels from 3D pseudo-folding graph representation of protein sequences using genetic algorithm-optimized support vector machines},
Author = {Michael Fernández and Leyden Fernández and José Abreu and Miguel Garriga},
Journal = {Journal of Molecular Graphics and Modelling},
Year = {2008},
Note = {cited By (since 1996) 3},
Number = {8},
Pages = {1306-1314},
Volume = {26},
Abstract = {Voltage-gated K+ ion channels (VKCs) are membrane proteins that regulate the passage of potassium ions through membranes. This work reports a classification scheme of VKCs according to the signs of three electrophysiological variables: activation threshold voltage (Vt), half-activation voltage (Va50) and half-inactivation voltage (Vh50). A novel 3D pseudo-folding graph representation of protein sequences encoded the VKC sequences. Amino acid pseudo-folding 3D distances count (AAp3DC) descriptors, calculated from the Euclidean distances matrices (EDMs) were tested for building the classifiers. Genetic algorithm (GA)-optimized support vector machines (SVMs) with a radial basis function (RBF) kernel well discriminated between VKCs having negative and positive/zero Vt, Va50 and Vh50 values with overall accuracies about 80, 90 and 86%, respectively, in crossvalidation test. We found contributions of the “pseudo-core” and “pseudo-surface” of the 3D pseudo-folded proteins to the discrimination between VKCs according to the three electrophysiological variables. © 2008 Elsevier Inc. All rights reserved.},
Affiliation = {Molecular Modeling Group, Center for Biotechnological Studies, Faculty of Agronomy, 44740 Matanzas, Cuba; Department of Bioscience and Bioinformatics, Kyushu Institute of Technology (KIT), 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan; Artificial Intelligence Lab, Faculty of Informatics, University of Matanzas, 44740 Matanzas, Cuba; Plant Biotechnology Group, Center for Biotechnological Studies, Faculty of Agronomy, 44740 Matanzas, Cuba},
Author_keywords = {Electrophysiological variables; Graph similarity; Ion channel; Kernel-based methods},
Comment = {http://www.scopus.com/inward/record.url?eid=2-s2.0-42749090642&partnerID=40&md5=01486f23c594fede840361bf77db5e8a http://www.ncbi.nlm.nih.gov/pubmed/18289899},
Document_type = {Article},
Doi = {http://dx.doi.org/10.1016/j.jmgm.2008.01.001},
Owner = {2008_J_Mol_Graph_Model_26_1306},
Source = {Scopus},
Url = {http://www.sciencedirect.com/science/article/pii/S1093326308000028}
}