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PePIP: a Pipeline for Peptide-Protein Interaction-site Prediction
Linköping University, Department of Physics, Chemistry and Biology.
2017 (English)Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesisAlternative title
PePIP : en Pipeline for Förutsägelse av Peptid-Protein Bindnings-site (Swedish)
Abstract [en]

Protein-peptide interactions play a major role in several biological processes, such as cellproliferation and cancer cell life-cycles. Accurate computational methods for predictingprotein-protein interactions exist, but few of these method can be extended to predictinginteractions between a protein and a particularly small or intrinsically disordered peptide.

In this thesis, PePIP is presented. PePIP is a pipeline for predicting where on a given proteina given peptide will most probably bind. The pipeline utilizes structural aligning to perusethe Protein Data Bank for possible templates for the interaction to be predicted, using thelarger chain as the query. The possible templates are then evaluated as to whether they canrepresent the query protein and peptide using a Random Forest classifier machine learningalgorithm, and the best templates are found by using the evaluation from the Random Forest in combination with hierarchical clustering. These final templates are then combined to givea prediction of binding site.

PePIP is proven to be highly accurate when testing on a set of 502 experimentally determinedprotein-peptide structures, suggesting a binding site on the correct part of the protein- surfaceroughly 4 out of 5 times.

Place, publisher, year, edition, pages
2017. , p. 40
Keywords [en]
PPI, Protein-protein interaction, Protein-peptide interaction, Random forest, Bioinformatics, Binding-site prediction, Structural Alignment
National Category
Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:liu:diva-138411ISRN: LITH-IFM-A-EX--17/3310--SEOAI: oai:DiVA.org:liu-138411DiVA, id: diva2:1110675
Subject / course
Chemical Biology
Presentation
2017-06-07, Nobel, B-Huset, Linköpings Universitet, Linköping, 13:15 (English)
Supervisors
Examiners
Available from: 2018-02-26 Created: 2017-06-16 Last updated: 2018-02-26Bibliographically approved

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