LiGIoNs: A Computational Method for the Detection and Classification of Ligand-Gated Ion Channels

Ligand-Gated Ion Channels (LGICs) are 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 uti-lizing features extracted solely from amino acid composition. However, special topo-logical characteristics of these proteins have not been utilized to date, which results in weaknesses regarding the correct class categorization of predicted proteins. Here we report the development of LiGIoNs, a profile Hidden Markov Model (pHMM) meth-od for the prediction and ligand-based classification of LGICs, utilizing their special topological characteristics. The method consists of a library of 35 pHMMs, built from the alignment of transmembrane segments of representative LGIC sequences. In ad-dition,14 Pfam pHMMs are used to further annotate and correctly classify unknown protein sequences into one of the 10 LGIC subfamilies. Evaluation of the method showed that it outperforms existent methods in the detection of LGICs. On top of that LiGIoNs is the only currently available method that classifies LGICs into sub-families. The method is available online at http://bioinformatics.biol.uoa.gr/ligions/.