Sequence analysis of membrane proteins with the Web server SPLIT

In this work, recently solved crystal structures of membrane proteins are e xamined with respect to the performance of the Web server SPLIT in predicti ng sequence location, conformation and orientation of membrane associated p olypeptide segments. The SPLIT predictor is based on the preference functio ns method. Preference functions serve to transform the input choice of amin o acid attributes into sequence dependent conformational preferences. Trans membrane helical segments are accurately predicted with a good selection of preference functions extracted from the compiled database of non-homologou s integral membrane proteins. Unlike other algorithms with similar high acc uracy, the SPLIT predictor requires no homology information. With preferenc e functions extracted from soluble proteins, the sequence location of short er non-transmembrane helices can be also found in membrane proteins. In par ticular, Richardson's preference functions are even better than hydrophobic moments in finding interface helices at the water/lipid phase boundary. Th e Internet access for the SPLIT system is at the address: http://pref.etfos .hr/split.