ppd901

\bibitem{ppd901} Sandor Vajda, and Dima Kozakov. Convergence and combination of methods in protein-protein docking // Current Opinion in Structural Biology, Volume 19, Issue 2, April 2009, Pages 164-170.

From SciDir Current Opinion in Structural Biology Volume 19, Issue 2, April 2009, Pages 164-170

Theory and simulation / Macromolecular assemblages doi:10.1016/j.sbi.2009.02.008

Convergence and combination of methods in protein–protein docking

Sandor Vajda^a, and Dima Kozakov^a

^aBiomolecular Engineering Research Center, Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA

Available online 25 March 2009.

The analysis of results from Critical Assessment of Predicted Interactions (CAPRI), the first community-wide experiment devoted to protein docking, shows that all successful methods consist of multiple stages. The methods belong to three classes: global methods based on fast Fourier transforms (FFTs) or geometric matching, medium-range Monte Carlo methods, and the restraint-guided High Ambiguity Driven biomolecular DOCKing (HADDOCK) program. Although these classes of methods require very different amounts of information in addition to the structures of component proteins, they all share the same four computational steps: firstly, simplified and/or rigid body search; secondly, selecting the region(s) of interest; thirdly, refinement of docked structures; and fourthly, selecting the best models. Although each method is optimal for a specific class of docking problems, combining computational steps from different methods can improve the reliability and accuracy of results.

Article Outline

Introduction

Multistage approach to docking

Rigid body and/or simplified geometry searches

Selecting the region(s) of interest

Refinement of docked structures

Final model selection

Strengths of the methods and of their combinations

Conclusions

Conflict of interest

References and recommended reading

Acknowledgements

References