For each protein target, several constructs are designed, using a standard protocol. If these are promising, but further optimization is needed, additional constructs could be designed in the same way. See the DNA cloning protocols page.
Amide hydrogen deuterium exchange with mass spectrometry.
HDX-MS can be used to identify the disordered N- and C-terminal regions that can be removed to further optimize the protein target. 
- Sharma S, Zheng ., Huang YJ, Ertekin A, Hamuro Y, Rossi P, Tejero R, Acton TB, Xiao R, Jiang M, Zhao L, Ma LC, Swapna, GV, Aramini JM, Montelioni GT (2009) Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry. Proteins 76: 882-894