http://www.rostlab.org/services/CHOP/
This is the closest I could find as a server for construct design. The
sample output does not show alignments though, only residue numbers.
It is better to design longer construct than short construct, because
missing critical terminal residues could lead to misfolding but having ~5
more hydrophilic residues wouldn't cause major problems ususally. They
could be either cleaved off during purification or simply disordered in
the structure.
HTH.
Holly
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