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

91 Scopus citations


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
StatePublished - 2011


  • interactome
  • protein docking
  • protein-protein interaction


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