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Issue 12, 2010
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Proteinprotein docking tested in blind predictions: the CAPRI experiment

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Abstract

Docking algorithms build multimolecular assemblies based on the subunit structures. “Unbound” docking, which starts with the free molecules and allows for conformation changes, may be used to predict the structure of a proteinprotein complex. This requires at least two steps, a rigid-body search that determines the relative position and orientation of the subunits, and a refinement step. The methods developed in the past twenty years yield native-like models in most cases, but always with many false positives that must be filtered out, and they fail when the conformation changes are large. CAPRI (Critical Assessment of PRedicted Interactions) is a community-wide experiment set up to monitor progress in the field. It offers participants the opportunity to test their methods in blind predictions that are assessed against an unpublished experimental structure. The models submitted by predictor groups are judged depending on how well they reproduce the geometry and the residue–residue contacts seen in the target structure. In nine years of CAPRI, 42 target complexes have been subjected to prediction based on the components' unbound structures. Good models have been submitted for 28 targets, and prediction has failed on 6. Both these successes and these failures have been fruitful, as they stimulated participant groups to develop new score functions to identify native-like solutions, and new algorithms that allow the molecules to be flexible during docking.

Graphical abstract: Protein–protein docking tested in blind predictions: the CAPRI experiment

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Publication details

The article was received on 12 Apr 2010, accepted on 18 May 2010 and first published on 19 Aug 2010


Article type: Review Article
DOI: 10.1039/C005060C
Citation: Mol. BioSyst., 2010,6, 2351-2362
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    Proteinprotein docking tested in blind predictions: the CAPRI experiment

    J. Janin, Mol. BioSyst., 2010, 6, 2351
    DOI: 10.1039/C005060C

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