Fernández M, Fernández L, Abreu JI, Garriga M. Classification of voltage-gated K(+) ion channels from 3D pseudo-folding graph representation of protein sequences using genetic algorithm-optimized support vector machines.
J Mol Graph Model 2008;
26:1306-14. [PMID:
18289899 DOI:
10.1016/j.jmgm.2008.01.001]
[Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2007] [Revised: 01/03/2008] [Accepted: 01/03/2008] [Indexed: 11/26/2022]
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(t)), 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.
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