Protein-protein docking with reduced potentials by exploiting multi-dimensional energy funnels

Conf Proc IEEE Eng Med Biol Soc. 2006:2006:5330-3. doi: 10.1109/IEMBS.2006.260790.

Abstract

We propose a new computational approach for protein docking exploiting energy funnels in the 6-dimensional space of translations and rotations of the ligand with respect to the receptor. Our approach consists of a series of translational and orientational moves of the ligand towards the receptor. Each move is performed using a global optimization method we have developed - the semi-definite underestimation (SDU) method - which can exploit a funnel-like energy function. We compared our approach with Monte Carlo on a set of 10 protein complexes using two residue-level potentials. To achieve the same level of performance (produce a near-native < or =3 A RMSD complex) our approach reduces energy evaluations by more than a factor of two, on average.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Cell Physiological Phenomena
  • Computational Biology / instrumentation*
  • Computational Biology / methods*
  • Computer Simulation
  • Databases, Protein
  • Ligands
  • Models, Molecular
  • Models, Theoretical
  • Monte Carlo Method
  • Protein Binding
  • Protein Conformation
  • Protein Interaction Mapping*
  • Proteins / chemistry*

Substances

  • Ligands
  • Proteins