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Updated: Sep 23, 2025

Capturing the Interaction Kinetics of an Ion Channel Protein with Small Molecules by the Bio-layer Interferometry Assay
Published on: March 7, 2018
LiGIoNs: A computational method for the detection and classification of ligand-gated ion channels
Avgi E Apostolakou1, Katerina C Nastou1, Georgios N Petichakis1
1Section of Cell Biology and Biophysics, Department of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, Athens 15701, Greece.
Abstract:
Ligand-Gated Ion Channels (LGICs) is one of the largest groups of transmembrane proteins. Due to their major role in synaptic transmission, both in the nervous system and the somatic neuromuscular junction, LGICs present attractive therapeutic targets. During the last few years, several computational methods for the detection of LGICs have been developed. These methods are based on machine learning approaches utilizing features extracted solely from the amino acid composition. Here we report the development of LiGIoNs, a profile Hidden Markov Model (pHMM) method for the prediction and ligand-based classification of LGICs. The method consists of a library of 10 pHMMs, one per LGIC subfamily, built from the alignment of representative LGIC sequences. In addition, 14 Pfam pHMMs are used to further annotate and classify unknown protein sequences into one of the 10 LGIC subfamilies. Evaluation of the method showed that it outperforms existing methods in the detection of LGICs. On top of that, LiGIoNs is the only currently available method that classifies LGICs into subfamilies. The method is available online at http://bioinformatics.biol.uoa.gr/ligions/.
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