Publication

PROPER: global protein interaction network alignment through percolation matching

Matthias Grossglauser, Seyed Hamed Hassani, Ehsan Kazemi, Hasan Pezeshgi Modarres
2016
Journal Articles

Abstract

Background The alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems. Network alignment can be used to transfer biological knowledge between species. Although different PI-network alignment algorithms were introduced during the last decade, developing an accurate and scalable algorithm that can find alignments with high biological and structural similarities among PPI networks is still challenging. Results In this paper, we introduce a new global network alignment algorithm for PPI networks called PROPER. Compared to other global network alignment methods, our algorithm shows higher accuracy and speed over real PPI datasets and synthetic networks. We show that the PROPER algorithm can detect large portions of conserved biological pathways between species. Also, using a simple parsimonious evolutionary model, we explain why PROPER performs well based on several different comparison criteria. Conclusions We highlight that PROPER has high potential in further applications such as detecting biological pathways, finding protein complexes and PPI prediction. The PROPER algorithm is available at http://proper.epfl.ch.

Official source

https://infoscience.epfl.ch/entities/publication/ac8d8c99-0679-46bd-b406-303f76765cc6

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Matthias Grossglauser, Seyed Hamed Hassani, Ehsan Kazemi, Hasan Pezeshgi Modarres
2016
Journal Articles

Abstract

Official source

https://infoscience.epfl.ch/entities/publication/ac8d8c99-0679-46bd-b406-303f76765cc6

About this result

Related concepts (32)

Structural alignment

Structural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules. In contrast to simple structural superposition, where at least some equivalent residues of the two structures are known, structural alignment requires no a priori knowledge of equivalent positions.

Protein–protein interaction

Protein–protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and the hydrophobic effect. Many are physical contacts with molecular associations between chains that occur in a cell or in a living organism in a specific biomolecular context. Proteins rarely act alone as their functions tend to be regulated.

AI alignment

In the field of artificial intelligence (AI), AI alignment research aims to steer AI systems towards humans' intended goals, preferences, or ethical principles. An AI system is considered aligned if it advances the intended objectives. A misaligned AI system pursues some objectives, but not the intended ones. It can be challenging for AI designers to align an AI system because it can be difficult for them to specify the full range of desired and undesired behaviors.

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