Convergence and combination of methods in protein–protein docking

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...

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Bibliographic Details
Published in:Current opinion in structural biology 2009-04, Vol.19 (2), p.164-170
Main Authors: Vajda, Sandor, Kozakov, Dima
Format: Article
Language:English
Subjects:
Algorithms
Computational Biology - methods
Computer Simulation
Databases, Protein
Monte Carlo Method
Protein Conformation
Protein Interaction Mapping - methods
Proteins - chemistry
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Summary: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.
ISSN:0959-440X
1879-033X
DOI:10.1016/j.sbi.2009.02.008