Empirical parameters for estimating protein-protein binding energies: number of short- and long-distance atom-atom contacts

Protein Pept Lett. 2008;15(2):223-31. doi: 10.2174/092986608783489634.

Abstract

The number of atom-atom contacts in long distance can fit to the experimental binding energies in a dataset containing 151 experimental data with the correlation coefficient about 0.68. Based on this factor, a set of distance-dependent empirical potentials for various types of short-distance (2.4 A-5 A) contacts was obtained by guided fitting, i.e. a set of two parameters fitting. Incorporation of these short-distance potentials improved the correlation coefficients to 0.881.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Databases, Protein
  • Models, Theoretical
  • Molecular Sequence Data
  • Protein Binding
  • Protein Conformation*
  • Proteins* / chemistry
  • Proteins* / metabolism
  • Statistics as Topic
  • Thermodynamics

Substances

  • Proteins