Predicting Protein Interaction Specificity using Sequence Harmony with Neighbour Support

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Predicting Protein Interaction Specificity using Sequence Harmony with Neighbour Support
status: finished
Master: project within::Bioinformatics
Student name: student name::Margriet Wassenaar
Dates
Start start date:=2012/01/09
End end date:=2013/01/31
Supervision
Supervisor: Anton Feenstra
Second supervisor: Qingzhen Hou
Thesis: has thesis::Media:Thesis.pdf
Poster: has poster::Media:Posternaam.pdf

Signature supervisor



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Abstract

About Predicting Protein Interaction Specificity using Sequence Harmony with Neighbour Support


Description

Prediction of protein-protein interactions (PPIs) is currently one of the most sought after goals in bioinformatics, and no method yet exists that can claim overall success in this area. The problem of identifying protein-protein interactions can be seen as the first major hurdle in the post-genomic era, and progress in that area will help us in understanding the mechanisms behind observed gene-gene interactions.

This project will continue to explore the relationship between the structure of (known) protein complexes and sequence specificity between interacting and non-interacting protein families. This specificity is crucial to many biological processes, and, for example, makes it possible that many signalling pathways and regulation mechanisms operate simultaneously inside the living cell. The specific aim will be to establish whether specificity patterns related to protein interactions are indeed detectable on a sequence level.

Previous analysis were performed using the default Sequence Harmony (SH) method. However, for specificity in general but certainly for specificity in PPI interface sites, support of neighbouring residues is known to be crucial. Recent additions to the SH method have incorporated several options for scoring neighbour support. The project will apply the extended SH method (SH+NB) to the existing PPI datasets and evaluate the efficacy of the SH+NB method for detecting interface residues.

Related projects:

Protein interactions and sequence specificity (Anita de Ruiter)

Sequence Harmony Statistics, Clustering and Secondary Structure (Esther Lips)

Analysis of Protein Interaction Specificity using Sequence Harmony with Neighbour Support (Susanne van de Ven)