Towards the prediction of protein interaction partners using physical docking

Molecular Systems Biology

Mark Nicholas Wass²  Gloria Fuentes²  Carles Pons¹  Florencio Pazos³ 

[1]Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain

[2]Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain

[3]Computational Systems Biology Group, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain

关键词: interactome;    protein docking;    protein–protein interaction;   

DOI  :  10.1038/msb.2011.3

来源: Wiley

【 摘 要 】

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.

【 授权许可】

CC BY-NC-SA   
Copyright © 2011 EMBO and Macmillan Publishers Limited

Creative Commons Attribution License, which permits distribution, and reproduction in any medium, provided the original author and source are credited. This license does not permit commercial exploitation without specific permission.