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. Author manuscript; available in PMC: 2014 Apr 8.
Published in final edited form as: Proteins. 2009 Jun;75(4):846–858. doi: 10.1002/prot.22293

Table II.

An example of the computational strategy

Protocol (Design Targets) Sequence Position Native sequence
recovery
99 100 101 102 103
Native sequence graphic file with name nihms131227ig1.jpg graphic file with name nihms131227ig2.jpg graphic file with name nihms131227ig3.jpg graphic file with name nihms131227ig2.jpg graphic file with name nihms131227ig4.jpg
Multi-constraint design (Bound & Free structures) graphic file with name nihms131227ig1.jpg F A graphic file with name nihms131227ig2.jpg graphic file with name nihms131227ig4.jpg 3/5
Single-constraint design (Bound structure) W W H M F 0/5
Single-constraint design (Free structure) graphic file with name nihms131227ig1.jpg F A H graphic file with name nihms131227ig4.jpg 2/5

The lowest scoring sequences selected in single- and multi-constraint simulations using the bound and free conformations of the germline antibody 7g12 and its native sequence. The CDR H3 loop positions shown were subjected to design.