PiType: A protein interaction type prediction cytoscape app.

[fgoebels]

Background

Protein interactions mediate a wide spectrum of functions in various cellular contexts. Functional versatility of protein complexes is due to a broad range of structural adaptations that determine their binding affinity, the number of interaction sites, and the lifetime. In terms of stability it has become customary to distinguish between obligate and non-obligate interactions dependent on whether or not the protomers can exist independently. In terms of spatio-temporal control protein interactions can be either simultaneously possible or mutually exclusive. PiType is a computational method for classifying protein interactions into simultaneously possible and mutually exclusive as well as into obligate and non-obligate (link to publication). The central advantage of PiType is that it's based on readily accessible features, such as sequence and functional properties of the two binding partners and their local network topology. Thus, PiType does not rely on atomic structures and is thus suitable for characterizing proteome-wide interaction data sets.

Goals

The goal of this project is to create a (Cytoscape app) for the PiType prediction tool (PiType demo can be found here). The app will allow researchers to automatically classify their loaded protein network into their respective interaction type and display the classified interactions in a new network. In this project it is open to the applicant to integrate novel resources or features for calculating the protein interaction types. One suggest resource that can be integrated is the STRING database.

Language Skills

Python, Java, Cytoscape

Difficulty level: 2

Ideally, the student would also be familiar with protein interaction concepts/terminology. Prior experience with Cytoscape is a plus.

Potential Mentors:

Florian Goebels, and Gary Bader

Contact

Florian Goebels

[tafodinho]

i will love to work on this project

[khanspers]

@tafodinho Please contact the mentor directly (florian.goebels@gmail.com), as questions posted here may go unnoticed.

[souravsingh]

@fgoebels I am interested in working on the project.

[fgoebels]

Sure Sourav. If you are interested you can send me a draft of your project proposal and I can give you feedback.

[khanspers]

GSoC 2017 selected project