Knowledge-based potentials in protein design

Alan M. Poole, Rama Ranganathan

Research output: Contribution to journalReview article

64 Scopus citations

Abstract

Knowledge-based potentials are statistical parameters derived from databases of known protein properties that empirically capture aspects of the physical chemistry of protein structure and function. These potentials play a key role in protein design by improving the accuracy of physics-based models of interatomic interactions and enhancing the computational efficiency of the design process by limiting the complexity of searching sequence space. Recently, knowledge-based potentials (in isolation or in combination with physics-based potentials) have been applied to the modification of existing protein function, the redesign of natural protein folds and the complete design of a non-natural protein fold. In addition, knowledge-based potentials appear to be providing important information about the global topology of amino acid interactions in natural proteins. A detailed study of the methods and products of these protein design efforts promises to greatly expand our understanding of proteins and the evolutionary process that created them.

Original languageEnglish (US)
Pages (from-to)508-513
Number of pages6
JournalCurrent Opinion in Structural Biology
Volume16
Issue number4
DOIs
StatePublished - Aug 1 2006

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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