Classification of voltage-gated K+ ion channels from 3D pseudo-folding graph representation of protein sequences using genetic algorithm-optimized support vector machines

Fernandez, Michael; Fernandez, Leyden; Abreu, Jose Ignacio; Garriga, Miguel

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 (V,), half-activation voltage (V-a50) and half-inactivation voltage (V-h50). 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 V-t, V-a50 and V-h50 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. (C) 2008 Elsevier Inc. All rights reserved.

Más información

Título según WOS: ID WOS:000256271600012 Not found in local WOS DB
Título de la Revista: JOURNAL OF MOLECULAR GRAPHICS AND MODELLING
Volumen: 26
Número: 8
Editorial: Elsevier
Fecha de publicación: 2008
Página de inicio: 1306
Página final: 1314
DOI:

10.1016/j.jmgm.2008.01.001

Notas: ISI