Supersite with proteomic tools
EMBLtools http://www.ebi.ac.uk/Tools/protein.html
Expasy proteomic tools http://ca.expasy.org/tools/
ProtScale  http://www.expasy.ch/cgi-bin/protscale.pl
sirw http://sirw.embl.de/
Smart http://smart.embl-heidelberg.de/