Protein design: A perspective from simple tractable models

Abstract

We review the recent progress in computational approaches to protein design which builds on advances in statistical-mechanical protein folding theory. In particular, we evaluate the degeneracy of the protein code (i.e. how many sequences fold into a given conformation) and outline a simple condition for ''designability`` in a protein model. From this point of view we discuss several popular protein models that were used for sequence design by several authors. We evaluate the strengths and weaknesses of popular approaches based on stochastic optimization in sequence space and discuss possible ways to improve them to bring them closer to experiment. We also discuss how sequence design affects folding and point out to some features of proteins that can be deigned ''in'' or designed ''out''}