Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces.

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2011-06-01

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Tunçbağ, Nurcan
KESKIN, O

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The vast majority of the chores in the living cell involve protein–protein interactions. Providing details of protein interactions at the residue level and incorporating them into protein interaction networks are crucial toward the elucidation of a dynamic picture of cells. Despite the rapid increase in the number of structurally known protein complexes, we are still far away from a complete network. Given experimental limitations, computational modeling of protein interactions is a prerequisite to proceed on the way to complete structural networks. In this work, we focus on the question ‘how do proteins interact?’ rather than ‘which proteins interact?’ and we review structure-based protein–protein interaction prediction approaches. As a sample approach for modeling protein interactions, PRISM is detailed which combines structural similarity and evolutionary conservation in protein interfaces to infer structures of complexes in the protein interaction network. This will ultimately help us to understand the role of protein interfaces in predicting bound conformations.

Subject Keywords

Hot-Spot Residues, Macromolecular Assemblies, Saccharomyces-Cerevisiae, Statistical-Analysis, Interaction Database, Interaction Networks, Recognition Sites, Crystalline State, Molecular Docking, Mass-Spectrometry

URI

https://hdl.handle.net/11511/32603

Journal

Physical biology

DOI

https://doi.org/10.1088/1478-3975/8/3/035006

Collections

Graduate School of Informatics, Article

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Citation Formats

N. Tunçbağ and O. KESKIN, “Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces.,” Physical biology, pp. 35006–35006, 2011, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/32603.