Knowledge-based potential functions in protein design

Predicting protein sequences that fold into specific native three-dimensional structures is a problem of great potential complexity. Although the complete solution is ultimately rooted in understanding the physical chemistry underlying the complex interactions between amino acid residues that determine protein stability, recent work shows that empirical information about these first principles is embedded in the statistics of protein sequence and structure databases. This review focuses on the use of ‘knowledge-based’ potentials derived from these databases in designing proteins. In addition, the data suggest how the study of these empirical potentials might impact our fundamental understanding of the energetic principles of protein structure. This review examines the ways in which knowledge-based potentials have been used to influence protein design and suggests that further study of the origin of these potentials may lead to a better understanding of the physical chemistry and proteins.