A simple and very efficient protein design strategy is proposed by developing some recently
introduced theoretical tools which have been successfully applied to exactly solvable protein
models. The design approach is implemented by using three amino acid classes and it is
based on the minimization of an appropriate energy function. For a given native state the
results of the design procedure are compared, through a statistical analysis, with the
properties of an ensemble of sequences folding in the same conformation. If the success …

Two of the most investigated problems in molecular biology are protein folding and design.
These problems stem from Anfinsen's discovery [1] that the sequence of amino acids of a
naturally-occurring protein uniquely specifies its thermodynamically stable native structure.
The protein folding challenge consists of predicting the native state of a protein from its
sequence of amino acids, while in protein design one is concerned to identify the amino acid
sequences folding into a pre-assigned native conformation. This last issue, having obvious …