Programs predict protein complexes

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The first extensive study demonstrating the ability to use computational docking programs to predict protein-protein interactions has been done through the use of facilities at the Barcelona Supercomputing Center. The research presented in the article Towards the prediction of protein interaction partners using physical docking, and published in the journal Molecular Systems Biology, was carried out by Mark Wass and Gloria Fuentes, from the Spanish National Cancer Research Centre (CNIO); Carles Pons from the Barcelona Supercomputer Center (BSC); and Florencio Pazos, from the Spanish National Centre for Biotechnology (CNB-CSIC), under the direction of Alfonso Valencia, head of the CNIO's Structural Biology and Biocomputing programme.

‘In this study, we showed for the first time that a docking method can be used to differentiate between interacting and non-interacting proteins. We observed that the score distribution of interacting proteins can be distinguished from that of non-interacting proteins. This finding was possible after running more than 100,000 docking experiments using the MareNostrum supercomputer,’ commented Carles Pons, from the BSC.

The authors used protein docking programs, which are normally used to model the details of the structure of complexes between proteins already known to interact, to detect the components of protein complexes scanning large collections of protein structures. Protein complexes are central to all the processes occurring in our cells, but to date only a small fraction of the composition and molecular details of their interaction have been characterised. This knowledge is essential for the understanding of the consequences of mutations and for the development of potential inhibitors.