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Prediction of Protein Interactions by Structural Matching: Prediction of PPI Networks and the Effects of Mutations on PPIs that Combines Sequence and Structural Information

  • Nurcan Tuncbag
  • Ozlem KeskinEmail author
  • Ruth Nussinov
  • Attila GursoyEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1558)

Abstract

Structural details of protein interactions are invaluable to the understanding of cellular processes. However, the identification of interactions at atomic resolution is a continuing challenge in the systems biology era. Although the number of structurally resolved complexes in the Protein Databank increases exponentially, the complexes only cover a small portion of the known structural interactome. In this chapter, we review the PRISM system that is a protein–protein interaction (PPI) prediction tool—its rationale, principles, and applications. We further discuss its extensions to discover the effect of single residue mutations, to model large protein assemblies, to improve its performance by exploiting conformational protein ensembles, and to reconstruct large PPI networks or pathway maps.

Key words

Structural matching PPI prediction Mutation mapping PPI network Structural pathway modeling 

Notes

Acknowledgments

N.T. thanks to the TUBITAK-Marie Curie Co-funded Brain Circulation Scheme (114C026) and the Young Scientist Award Program of the Science Academy (Turkey) for the support. O.K and A.G. are members of the Science Academy (Turkey). We acknowledge the partial funding from TUBITAK projects (114M196 and 113E164). This project has been funded in whole or in part with Federal funds from the Frederick National Laboratory for Cancer Research, National Institutes of Health, under contract HHSN261200800001E. This research was supported [in part] by the Intramural Research Program of NIH, Frederick National Lab, Center for Cancer Research.

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  1. 1.Graduate School of Informatics, Department of Health InformaticsMiddle East Technical UniversityAnkaraTurkey
  2. 2.Chemical and Biological Engineering, College of EngineeringKoc UniversityIstanbulTurkey
  3. 3.Center for Computational Biology and BioinformaticsKoc UniversityIstanbulTurkey
  4. 4.Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National LaboratoryNational Cancer InstituteFrederickUSA
  5. 5.Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Institute of Molecular MedicineTel Aviv UniversityTel AvivIsrael
  6. 6.Computer Engineering, College of EngineeringKoc UniversityIstanbulTurkey

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