SNARER

SNARER is a predictor for SNARE proteins (SNARE stands for Soluble N–ethylmaleimide sensitive factor attachment protein receptor), part of a superfamily of proteins involved in the mechanism of molecular trafficking and it includes members from yeasts to mammalian cells. Vesicle-mediated transport is essential for several processes at the base of the cell, such as the secretion of proteins and hormones, the release of neurotransmitters, the phagocytosis of pathogens by the immune system and the transport of between cellular compartments. In recent years, attention to SNARE proteins has increased following some scientific studies which have shown the implication of SNAREs in some neural disorders due to their crucial role in the neuronal and neurosensory release during the traffic of the vesicles with substances which act as neurotransmitters. The current challenge is to be able to identify, through increasingly accurate prediction methods, the function of unknown proteins. This is an advantage for expanding our knowledge of the biological roles of proteins in the pathways in which they are involved. The classification allows to identify which category a new observed data belongs to, on the basis of a training data set, of which the category it is known. In the classification problems of protein sequences it is useful to convert the sequences of different lengths into a fixed length numerical vector using different protein descriptors. On the basis of the chemical-physical, electrical and energy charge characteristics of the SNARES, 19 descriptors have been adopted for the prediction (signal sequence helical potential,the Chou-Fasman parameter of the coil conformation,a parameter of charge transfer capability,a parameter of charge transfer donor capability, normalized frequency of N-terminal helix, normalized frequency of C-terminal helix, normalized frequency of N-terminal non helical region, normalized frequency of C-terminal non helical region, solvation free energy, localized electrical effect, positive charge, negative charge, partition energy, average accessible surface area, side chain interaction parameter, bulkiness, helix formation parameters delta delta G, sheet and helix probability).