Naslov
Sequence Analysis of Membrane Proteins with the Web Server Split

Autori
Juretić, Davor ; Jerončić, Ana ; Zucić, Damir

Izvornik
Croatica Chemica Acta (0011-1643) 72 (1999), 4; 975-997

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
sequence analysis ; membrane proteins ; prediction ; secondary structure ; preference functions ; transmembrane helix ; interface helix ; hydrophobic moments ; antibacterial peptides

Sažetak
In this work recently solved crystal structures of membrane proteins are examined with respect to the performance of the Web server SPLIT in predicting sequence location, conformation and orientation of membrane associated polypeptide segments. The SPLIT predictor is based on the preference functions method. Preference functions serve to transform the input choice of amino acid attributes into sequence dependent conformational preferences. Transmembrane helical segments are accurately predicted with a good selection of preference functions extracted from compiled database of non-homologous integral membrane proteins. Unlike other algorithms with similar high accuracy, the SPLIT predictor does not require homology information. With preference functions extracted from soluble proteins the sequence location of shorter non-transmembrane helices can be also found in membrane proteins. In particular, Richardson's preference functions are even better than hydrophobic moments in finding interface helices at water/lipid phase boundary. The Internet access for the system SPLIT is at the address: http://pref.etfos.hr/split

Izvorni jezik
Engleski

Znanstvena područja
Fizika

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