El-Kebir M, Marschall T, Wohlers I, Patterson M, Heringa J, Schönhuth A, Klau GW. Mapping proteins in the presence of paralogs using units of coevolution.
BMC Bioinformatics 2014;
14 Suppl 15:S18. [PMID:
24564758 PMCID:
PMC3852051 DOI:
10.1186/1471-2105-14-s15-s18]
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Abstract
Background
We study the problem of mapping proteins between two protein families in the presence of paralogs. This problem occurs as a difficult subproblem in coevolution-based computational approaches for protein-protein interaction prediction.
Results
Similar to prior approaches, our method is based on the idea that coevolution implies equal rates of sequence evolution among the interacting proteins, and we provide a first attempt to quantify this notion in a formal statistical manner. We call the units that are central to this quantification scheme the units of coevolution. A unit consists of two mapped protein pairs and its score quantifies the coevolution of the pairs. This quantification allows us to provide a maximum likelihood formulation of the paralog mapping problem and to cast it into a binary quadratic programming formulation.
Conclusion
CUPID, our software tool based on a Lagrangian relaxation of this formulation, makes it, for the first time, possible to compute state-of-the-art quality pairings in a few minutes of runtime. In summary, we suggest a novel alternative to the earlier available approaches, which is statistically sound and computationally feasible.
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