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Mol Syst Biol. 2011 Feb 15;7:469. doi: 10.1038/msb.2011.3.

Towards the prediction of protein interaction partners using physical docking.

Author information

1
Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre, Madrid, Spain.

Abstract

Deciphering the whole network of protein interactions for a given proteome ('interactome') is the goal of many experimental and computational efforts in Systems Biology. Separately the prediction of the structure of protein complexes by docking methods is a well-established scientific area. To date, docking programs have not been used to predict interaction partners. We provide a proof of principle for such an approach. Using a set of protein complexes representing known interactors in their unbound form, we show that a standard docking program can distinguish the true interactors from a background of 922 non-redundant potential interactors. We additionally show that true interactions can be distinguished from non-likely interacting proteins within the same structural family. Our approach may be put in the context of the proposed 'funnel-energy model'; the docking algorithm may not find the native complex, but it distinguishes binding partners because of the higher probability of favourable models compared with a collection of non-binders. The potential exists to develop this proof of principle into new approaches for predicting interaction partners and reconstructing biological networks.

PMID:
21326236
PMCID:
PMC3063693
DOI:
10.1038/msb.2011.3
[Indexed for MEDLINE]
Free PMC Article

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