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. Author manuscript; available in PMC: 2008 Aug 15.
Published in final edited form as: Biochemistry. 2006 Oct 17;45(41):12547–12559. doi: 10.1021/bi060857u

Figure 2. Hierarchical design protocol.

Figure 2

(1) The search of the largest space is done with an approximate energy function which obeys all the constraints of the discrete search algorithms DEE and A*. (2) The top results from the approximate search are re-evaluated with a more accurate energy function which may include term that are more expensive or that are incompatible with the search algorithms used in the first step. (3) The best candidates are subjected to more detailed evaluations, including estimation of additional properties such as specificity of binding. (4) Only the top selections from the final evaluation are passed on for experimental evaluation.