Selected protein design references

• Desjarlais JR, Clarke ND. Computer search algorithms in protein modification and design. Curr Opin Struct Biol. 1998 Aug;8(4):471-5. PubMed
  Old, but good basics.

• Looger LL, Hellinga HW. Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics. J Mol Biol. 2001 Mar 16;307(1):429-45. PubMed
  On dead end elimination.

• S. M. Larson, J. England, J. DesJarlais, and V. S. Pande. Thoroughly sampling sequence space: large-scale protein design of structural ensembles. Protein Science 11 2804-281 (2002). Protein Science
  Applies a genetic algorithm on a large scale.

• Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, Baker D. Design of a novel globular protein fold with atomic-level accuracy. Science. 2003 Nov 21;302(5649):1364-8. PubMed
  A recent high profile application, though some argue the fold's not "novel."

• Voigt CA, Mayo SL, Arnold FH, Wang ZG. Computational method to reduce the search space for directed protein evolution. Proc Natl Acad Sci U S A. 2001 Mar 27;98(7):3778-83. PNAS
  Mean field theory applied to design.