FastContact: rapid estimate of contact and binding free energies

Bioinformatics. 2005 May 15;21(10):2534-6. doi: 10.1093/bioinformatics/bti322. Epub 2005 Feb 15.

Abstract

Interaction free energies are crucial for analyzing binding propensities in proteins. Although the problem of computing binding free energies remains open, approximate estimates have become very useful for filtering potential binding complexes. We report on the implementation of a fast computational estimate of the binding free energy based on a statistically determined desolvation contact potential and Coulomb electrostatics with a distance-dependent dielectric constant, and validated in the Critical Assessment of PRotein Interactions experiment. The application also reports residue contact free energies that rapidly highlight the hotspots of the interaction.

Availability: The program was written in Fortran. The executable and full documentation is freely available at http://structure.pitt.edu/software/FastContact

MeSH terms

  • Algorithms*
  • Amino Acids / chemistry*
  • Binding Sites
  • Computer Simulation
  • Models, Chemical*
  • Models, Molecular*
  • Protein Binding
  • Protein Conformation
  • Protein Interaction Mapping / methods*
  • Proteins / analysis
  • Proteins / chemistry*
  • Sequence Analysis, Protein / methods*
  • Software

Substances

  • Amino Acids
  • Proteins