title: Knowledge-based potentials in protein design.
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.
authors.affiliation: Howard Hughes Medical Institute, Department of Pharmacology and the Green Comprehensive Center Division for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9050, USA.
authors.forename: Alan M
authors.initials: AM
authors.lastname: Poole
authors.forename: Rama
authors.initials: R
authors.lastname: Ranganathan
mesh_terms: D030562:Databases, Protein; D015202:Protein Engineering; D011506:Proteins / Q000737:chemistry* / Q000235:genetics* / Q000502:physiology*
chemical_list: D011506:Proteins