Models of Protein Structure and Function Used in Protein Design
Protein design can be accomplished using computer models, which, while simplifying the problem, are able to generate sequences that fold to the desired structure. Computational protein design algorithms search the sequence-conformation space for sequences that are low in energy when folded to the target structure. This search space is large; currently the most challenging requirement for computational protein design is a fast, yet accurate, energy function that can distinguish optimal sequences from similar suboptimal ones.
Computational protein design algorithms use rotamer libraries and models of protein energetics to evaluate how mutations would affect a protein's structure and function. These energy functions typically include a combination of molecular mechanics, statistical (i.e. knowledge-based), and other empirical terms. However, the trend has been towards using more physically based potential energy functions.
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