Protein docking using continuum electrostatics and geometric fit

Jeffrey G. Mandell, Victoria A. Roberts, Michael E. Pique, Vladimir Kotlovyi, Julie C. Mitchell, Erik Nelson, Igor Tsigelny, Lynn F. Ten Eyck

Research output: Contribution to journalArticlepeer-review

274 Scopus citations

Abstract

The computer program DOT quickly finds low-energy docked structures for two proteins by performing a systematic search over six degrees of freedom. A novel feature of DOT is its energy function, which is the sum of both a Poisson-Boltzmann electrostatic energy and a van der Waals energy, each represented as a grid-based correlation function. DOT evaluates the energy of interaction for many orientations of the moving molecule and maintains separate lists scored by either the electrostatic energy, the van der Waals energy or the composite sum of both. The free energy is obtained by summing the Boltzmann factor over all rotations at each grid point. Three important findings are presented. First, for a wide variety of protein-protein interactions, the composite-energy function is shown to produce larger clusters of correct answers than found by scoring with either van der Waals energy (geometric fit) or electrostatic energy alone. Second, free-energy clusters are demonstrated to be indicators of binding sites. Third, the contributions of electrostatic and attractive van der Waals energies to the total energy term appropriately reflect the nature of the various types of protein-protein interactions studied.

Original languageEnglish
Pages (from-to)105-113
Number of pages9
JournalProtein Engineering
Volume14
Issue number2
DOIs
StatePublished - 2001
Externally publishedYes

Keywords

  • Convolution
  • Partition function
  • Poisson-Boltzmann
  • Protein-protein interactions
  • Structure prediction

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