Abstract
Ion channels (IC) are ion-permeable protein pores located in the lipid membranes of all cells. Different ion channels have unique functions in different biological processes. Due to the rapid development of high-throughput mass spectrometry, proteomic data are rapidly accumulating and provide us an opportunity to systematically investigate and predict ion channels and their types. In this paper, we constructed a support vector machine (SVM)-based model to quickly predict ion channels and their types. By considering the residue sequence information and their physicochemical properties, a novel feature-extracted method which combined dipeptide composition with the physicochemical correlation between two residues was employed. A feature selection strategy was used to improve the performance of the model. Comparison results of in jackknife cross-validation demonstrated that our method was superior to other methods for predicting ion channels and their types. Based on the model, we built a web server called IonchanPred which can be freely accessed from http://lin.uestc.edu.cn/server/IonchanPredv2.0.
Highlights
IntroductionIon channels exist in the membranes of all cells and are required in numerous physiological and pathological processes, such as regulating neuronal and cardiac excitability, muscle contraction, hormone secretion, fluid movement, and immune cell activation [1]
Ion channels are pore-forming membrane proteins for the transmembrane exchange of inorganic ions
The sequences of ion channels were collected from the Universal Protein Resource (UniProt) [19] and the Ligand-Gated Ion channel database [20]
Summary
Ion channels exist in the membranes of all cells and are required in numerous physiological and pathological processes, such as regulating neuronal and cardiac excitability, muscle contraction, hormone secretion, fluid movement, and immune cell activation [1]. Due to their important role in biological processes, ion channels are often used as targets for disease diagnosis and drug development. The opening and closing of the voltage-gated ion channels depends on the change of the membrane potential, whereas the state of the ligand channels is closely related to the binding of the ligand. The voltage-gated ion channels can be further classified into the following four subclasses: potassium (K+ ), sodium (Na+ ), calcium (Ca2+ ), and anion channels
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