Ionic channels belong to the group of the most important proteins. Not only do they enable transmembrane transport but they are also the key factors for proper cell function. Mutations changing their structure and functionality often lead to severe diseases called channelopathies. On the other hand, transmembrane channels are very difficult objects for experimental studies. Only 2% of experimentally identified structures are transmembrane proteins, while genomic studies show that transmembrane proteins make up 30% of all coded proteins. This gap could be diminished by bioinformatical methods which enable modeling unknown protein structures, functions, transmembrane location, and ligand binding. Several in silico methods dedicated to transmembrane proteins have been developed; some general methods could also be used. They provide the information unavailable from experiments. Current modeling tools use a variety of computational methods, which provide results of surprisingly high quality.