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/