Accounting for global protein deformability during protein-protein and protein-ligand docking

Biochim Biophys Acta. 2005 Dec 30;1754(1-2):225-31. doi: 10.1016/j.bbapap.2005.07.045. Epub 2005 Sep 12.

Abstract

Computational docking methods are valuable tools aimed to simplify the costly process of drug development and improvement. Most current approaches assume a rigid receptor structure to allow virtual screening of large numbers of possible ligands and putative binding sites on a receptor molecule. However, inclusion of receptor flexibility can be of critical importance since binding of a ligand can lead to changes in the receptor protein conformation that are sterically necessary to accommodate a ligand. Recent approaches to efficiently account for receptor flexibility during docking simulations are reviewed. In particular, accounting efficiently for global conformational changes of the protein backbone during docking is a still challenging unsolved problem. An approximate method has recently been suggested that is based on relaxing the receptor conformation during docking in pre-calculated soft collective degrees of freedom (M. Zacharias, Rapid protein-ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: binding of FK506 to FKBP, Proteins: Struct., Funct., Genet. 54 (2004) 759-767). Test applications on protein-protein docking and on docking the inhibitor staurosporine to the apo-form of cAMP-dependent protein kinase A catalytic domain indicate significant improvement of docking results compared to rigid docking at a very modest computational demand. Accounting for receptor conformational changes in pre-calculated global degrees of freedom might offer a promising route to improve systematic docking screening simulations.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Binding Sites
  • Computer Simulation
  • Cyclic AMP-Dependent Protein Kinases / chemistry
  • Cyclic AMP-Dependent Protein Kinases / metabolism
  • Ligands*
  • Models, Molecular
  • Protein Binding
  • Protein Conformation*
  • Protein Structure, Tertiary / drug effects
  • Proteins / chemistry*
  • Proteins / metabolism
  • Staurosporine / chemistry
  • Staurosporine / metabolism

Substances

  • Ligands
  • Proteins
  • Cyclic AMP-Dependent Protein Kinases
  • Staurosporine