Protein design is NP-hard

Abstract

Biologists working in the area of computational protein design have never doubted the seriousness of the algorithmic challenges that face them in attempting in silico sequence selection. It turns out that in the language of the computer science community, this discrete optimization problem is NP-hard. The purpose of this paper is to explain the context of this observation, to provide a simple illustrative proof and to discuss the implications for future progress on algorithms for computational protein design.