Knowledge-based potential functions in protein design

Curr Opin Struct Biol. 2002 Aug;12(4):447-52. doi: 10.1016/s0959-440x(02)00346-9.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Amino Acid Sequence
  • Amino Acids / chemistry
  • Artificial Intelligence*
  • Conserved Sequence
  • Databases, Protein*
  • Information Storage and Retrieval / methods
  • Molecular Sequence Data
  • Protein Conformation*
  • Protein Engineering / methods*
  • Protein Folding
  • Proteins / chemistry*
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / methods

Substances

  • Amino Acids
  • Proteins