title: iCTX-type: a sequence-based predictor for identifying the types of conotoxins in targeting ion channels.
abstract: Conotoxins are small disulfide-rich neurotoxic peptides, which can bind to ion channels with very high specificity and modulate their activities. Over the last few decades, conotoxins have been the drug candidates for treating chronic pain, epilepsy, spasticity, and cardiovascular diseases. According to their functions and targets, conotoxins are generally categorized into three types: potassium-channel type, sodium-channel type, and calcium-channel types. With the avalanche of peptide sequences generated in the postgenomic age, it is urgent and challenging to develop an automated method for rapidly and accurately identifying the types of conotoxins based on their sequence information alone. To address this challenge, a new predictor, called iCTX-Type, was developed by incorporating the dipeptide occurrence frequencies of a conotoxin sequence into a 400-D (dimensional) general pseudoamino acid composition, followed by the feature optimization procedure to reduce the sample representation from 400-D to 50-D vector. The overall success rate achieved by iCTX-Type via a rigorous cross-validation was over 91%, outperforming its counterpart (RBF network). Besides, iCTX-Type is so far the only predictor in this area with its web-server available, and hence is particularly useful for most experimental scientists to get their desired results without the need to follow the complicated mathematics involved.
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Ding
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors.forename: En-Ze
authors.initials: EZ
authors.lastname: Deng
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors.forename: Lu-Feng
authors.identifier: 0000-0003-0081-2271
authors.initials: LF
authors.lastname: Yuan
authors.affiliation: Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China.
authors.forename: Li
authors.initials: L
authors.lastname: Liu
authors.affiliation: Key Laboratory for Neuro-Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China ; Gordon Life Science Institute, Boston, MA 02478, USA.
authors.forename: Hao
authors.identifier: 0000-0003-3057-8586
authors.initials: H
authors.lastname: Lin
authors.affiliation: Gordon Life Science Institute, Boston, MA 02478, USA ; Department of Physics, School of Sciences Center for Genomics and Computational Biology, Hebei United University, Tangshan 063000, China.
authors.forename: Wei
authors.identifier: 0000-0002-6857-7696
authors.initials: W
authors.lastname: Chen
authors.affiliation: Gordon Life Science Institute, Boston, MA 02478, USA ; Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors.forename: Kuo-Chen
authors.initials: KC
authors.lastname: Chou
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D015220:Calcium Channels / Q000737:chemistry / Q000187:drug effects; D020916:Conotoxins / Q000737:chemistry / Q000145:classification / Q000378:metabolism*; D006801:Humans; D009479:Neuropeptides / Q000737:chemistry / Q000145:classification / Q000378:metabolism*; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D015221:Potassium Channels / Q000737:chemistry / Q000187:drug effects; D015222:Sodium Channels / Q000737:chemistry / Q000187:drug effects
chemical_list: D000596:Amino Acids; D015220:Calcium Channels; D020916:Conotoxins; D009479:Neuropeptides; D010455:Peptides; D015221:Potassium Channels; D015222:Sodium Channels