Protein design based on the relative entropy

Phys Rev E Stat Nonlin Soft Matter Phys. 2006 Jun;73(6 Pt 1):061903. doi: 10.1103/PhysRevE.73.061903. Epub 2006 Jun 2.

Abstract

An approach to protein design is proposed based on the relative entropy and a reduced amino acid alphabet. In this approach, the relative entropy is used as a minimization object function. The method has been tested on a real protein's off-lattice model successfully, and the results are similar to those obtained from other design studies. It can be applied as a uniform frame for both folding and inverse folding of protein. An iterative calculation method of the ensemble average of the contact strength is proposed at the same time.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acids / chemistry
  • Databases, Protein
  • Entropy*
  • Monte Carlo Method
  • Proteins / chemistry*

Substances

  • Amino Acids
  • Proteins