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Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing
Published on: October 3, 2018
Interrogating domain-domain interactions with parsimony based approaches.
Katia S Guimarães1, Teresa M Przytycka
1National Center of Biotechnology, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. katiaguim@gmail.com
BMC Bioinformatics
|March 28, 2008
Summary
A new Generalized Parsimonious Explanation (GPE) method improves prediction of protein domain interactions. This method is competitive with top algorithms and offers new insights into domain interaction properties.
Area of Science:
- Computational Biology
- Bioinformatics
- Protein Interaction Networks
Background:
- Identifying interacting domain pairs is crucial for understanding protein interactions.
- Existing methods for predicting domain interactions have limitations.
- Understanding these limitations is key to developing improved prediction approaches.
Purpose of the Study:
- To introduce and evaluate the Generalized Parsimonious Explanation (GPE) method for predicting domain-domain interactions.
- To compare the performance of GPE with existing methods.
- To investigate the properties of domain interactions mediating protein interactions in a network.
Main Methods:
- Developed the Generalized Parsimonious Explanation (GPE) method, an extension of the Parsimonious Explanation (PE) method.
- GPE adjusts domain definition granularity and allows differential costs for domain interactions.
- Utilized a combinatorial counting approach to survey domain interactions.
Main Results:
- The GPE method demonstrates competitive performance against top domain interaction prediction algorithms, despite using less information.
- Identified a propensity for co-occurring domains and homo-domains in mediating protein interactions.
- Found that the overrepresentation of these special domain pairs is lower than in the iPfam dataset.
Conclusions:
- The Generalized Parsimonious Explanation (GPE) approach offers a novel method for predicting and analyzing domain-domain interactions.
- Protein interaction networks show a significant deviation in domain interaction properties compared to iPfam data.
- This deviation is observed under the assumption that all protein interactions are mediated by domain interactions.
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