Interrogating domain-domain interactions with parsimony based approaches

Background: The identification and characterization of interacting domain pairs is an important step towards understanding protein interactions. In the last few years, several methods to predict domain interactions have been proposed. Understanding the power and the limitations of these methods is key to the development of improved approaches and better understanding of the nature of these interactions. Results: Building on the previously published Parsimonious Explanation method (PE) to predict domain-domain interactions, we introduced a new Generalized Parsimonious Explanation (GPE) method, which (i) adjusts the granularity of the domain definition to the granularity of the input data set and (ii) permits domain interactions to have different costs. This allowed for preferential selection of the so-called "co-occurring domains" as possible mediators of interactions between proteins. The performance of both variants of the parsimony method are competitive to the performance...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Katia S. Guimarães, Teresa M. Przytycka
• Keywords: BMCBI 2008, Domain Interactions, Generalized Parsimonious Explanation, Parsimonious Explanation