InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical research.
Virtually all the biological processes that occur inside or outside cells are mediated by protein-protein interactions (PPIs). Hence, the charting and description of the PPI network, initially in organisms, the interactome, but more recently in specific tissues, is essential to fully understand cellular processes both in health and disease. The study of PPIs is also at the heart of renewed efforts in the medical and biotechnological arena in the quest of new therapeutic targets and drugs. Here, we present a mini review of 11 computational tools and resources tools developed by us to address different aspects of PPIs: from interactome level to their atomic 3D structural details. We provided details on each specific resource, aims and purpose and compare with equivalent tools in the literature. All the tools are presented in a centralized, one-stop, web site: InteractoMIX (http://interactomix.com).
Structural Bioinformatics Lab (GRIB-IMIM), Department of Experimental and Health Science, University Pompeu Fabra, Barcelona 08005, Catalonia, Spain.
Daniel
D
Poglayen
Structural Bioinformatics Lab (GRIB-IMIM), Department of Experimental and Health Science, University Pompeu Fabra, Barcelona 08005, Catalonia, Spain.
Manuel Alejandro
MA
Marín-López
Structural Bioinformatics Lab (GRIB-IMIM), Department of Experimental and Health Science, University Pompeu Fabra, Barcelona 08005, Catalonia, Spain Laboratory of Protein Design & Immunoengineering, School of Engineering, Ecole Polytechnique Federale de Lausanne, Lausanne 1015, Vaud, Switzerland.
Jaume
J
Bonet
Structural Bioinformatics Lab (GRIB-IMIM), Department of Experimental and Health Science, University Pompeu Fabra, Barcelona 08005, Catalonia, Spain Centre for Molecular Medicine and Therapeutics at the Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada V5Z 4H4.
Oriol
O
Fornes
Structural Bioinformatics Lab (GRIB-IMIM), Department of Experimental and Health Science, University Pompeu Fabra, Barcelona 08005, Catalonia, Spain.
Javier
J
Garcia-Garcia
Division of Metabolic and Vascular Health, University of Warwick, Coventry CV4 7AL, U.K.
Joan
J
Planas-Iglesias
GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC), Madrid 28049, Spain.
Joan
J
Segura
Structural Bioinformatics Lab (GRIB-IMIM), Department of Experimental and Health Science, University Pompeu Fabra, Barcelona 08005, Catalonia, Spain baldo.oliva@upf.edu narcis.fernandez@gmail.com.
Baldo
B
Oliva
Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, U.K. baldo.oliva@upf.edu narcis.fernandez@gmail.com.
Narcis
N
Fernandez-Fuentes
D035843:Biomedical Research; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D056890:Eukaryota / Q000378:metabolism; D006801:Humans; D025941:Protein Interaction Mapping
computational predictions; databases; protein–protein interactions; structural bioinformatics; web-servers