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
