Towards the prediction of protein interaction partners using physical docking

Mark Nicholas Wass, Gloria Fuentes, Carles Pons, Florencio Pazos, Alfonso Valencia

Research output: Contribution to journalArticlepeer-review

86 Scopus citations

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.

Original languageEnglish (US)
Article number469
JournalMolecular Systems Biology
Volume7
DOIs
StatePublished - 2011

Keywords

  • interactome
  • protein docking
  • protein-protein interaction

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