Galaxy InteractoMIX: An Integrated Computational Platform for the Study of Protein–Protein Interaction Data. Issue 11 (28th May 2021)

• Record Type: Journal Article
• Authors: Mirela-Bota, Patricia; Aguirre-Plans, Joaquim; Meseguer, Alberto; Galletti, Cristiano; Segura, Joan; Planas-Iglesias, Joan; Garcia-Garcia, Javi; Guney, Emre; Oliva, Baldo; Fernandez-Fuentes, Narcis
• Is Part Of: Journal of molecular biology. Volume 433:Issue 11(2021)
• Publication Date: 2021-05-28
• Subjects: interactomics -- network analyses -- integration -- Galaxy platform -- workflows; PPI protein–protein interaction -- RF random forest; Molecular biology -- Periodicals; Biology -- Periodicals; Biochemistry -- Periodicals; Bacteriology -- Periodicals; Molecular Biology -- Periodicals; Biochemistry -- Periodicals; Biologie moléculaire -- Périodiques; Biologie -- Périodiques; Biochimie -- Périodiques; Moleculaire biologie; Biochemistry; Biology; Molecular biology; Periodicals; 572.805
• DOI: 10.1016/j.jmb.2020.09.015
• Languages: English
• ISSNs: 0022-2836

Abstract

Abstract: Protein interactions play a crucial role among the different functions of a cell and are central to our understanding of cellular processes both in health and disease. Here we present Galaxy InteractoMIX (http://galaxy.interactomix.com ), a platform composed of 13 different computational tools each addressing specific aspects of the study of protein–protein interactions, ranging from large-scale cross-species protein-wide interactomes to atomic resolution level of protein complexes. Galaxy InteractoMIX provides an intuitive interface where users can retrieve consolidated interactomics data distributed across several databases or uncover links between diseases and genes by analyzing the interactomes underlying these diseases. The platform makes possible large-scale prediction and curation protein interactions using the conservation of motifs, interology, or presence or absence of key sequence signatures. The range of structure-based tools includes modeling and analysis of protein complexes, delineation of interfaces and the modeling of peptides acting as inhibitors of protein–protein interactions. Galaxy InteractoMIX includes a range of ready-to-use workflows to run complex analyses requiring minimal intervention by users. The potential range of applications of the platform covers different aspects of life science, biomedicine, biotechnology and drug discovery where protein associations are studied. Graphical abstract: Unlabelled Image Highlights: A centralized, one-stop, resource that covers a wide range of computational analyses from proteome-wide interactomes to structure of protein complexes. Multiscale analyses and modeling from pathways associated with pathologies to molecular details of interactions. A resource implemented in the Galaxy platform benefitting from all the advantages associated with it (e.g. re-usability, reproducibility, workflow editor, job history, etc.) A range of ready-to-use workflows available to use to perform advance and complex data analyses together with a range of tutorials to familiarize users with the platform. An easy-to-use, web-based resource allowing non-computational researchers to perform complex analyses of interactomics data.