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RADI (Reduced Alphabet Direct Information): Improving execution time for direct-coupling analysis

Bernat Anton, Mireia Besalú, Oriol Fornes, Jaume Bonet, Gemma De las Cuevas, Narcís Fernández-Fuentes, View ORCID ProfileBaldo Oliva
doi: https://doi.org/10.1101/406603
Bernat Anton
1Structural Bioinformatics Lab (GRIB-IMIM), Department of Experimental and Health Science, University Pompeu Fabra, Barcelona 08005, Catalonia, Spain
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Mireia Besalú
2Departament de Matemàtiques i Informàtica, Universitat de Barcelona, Catalonia, Spain
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Oriol Fornes
1Structural Bioinformatics Lab (GRIB-IMIM), Department of Experimental and Health Science, University Pompeu Fabra, Barcelona 08005, Catalonia, Spain
3Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, BC Children’s Hospital Research Institute, University of British Columbia, 950 28th Ave W, Vancouver, BC V5Z 4H4, Canada
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Jaume Bonet
1Structural Bioinformatics Lab (GRIB-IMIM), Department of Experimental and Health Science, University Pompeu Fabra, Barcelona 08005, Catalonia, Spain
4Laboratory of Protein Design & Immunoengineering, School of Engineering, Ecole Polytechnique Federale de Lausanne, Lausanne 1015, Vaud, Switzerland
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Gemma De las Cuevas
5Institut für Theoritische Physik, School of Mathematics, Computer Science and Physics, Universität Innsbruck. A-6020 Innsbruck, Austria
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Narcís Fernández-Fuentes
6Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY233EB Aberystwyth, United Kingdom
7Department of Biosciences, U Science Tech, Universitat de Vic-Universitat Central de Catalunya, Vic 08500, Catalonia, Spain
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Baldo Oliva
1Structural Bioinformatics Lab (GRIB-IMIM), Department of Experimental and Health Science, University Pompeu Fabra, Barcelona 08005, Catalonia, Spain
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  • ORCID record for Baldo Oliva
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Abstract

Motivation Direct-coupling analysis (DCA) for studying the coevolution of residues in proteins has been widely used to predict the three-dimensional structure of a protein from its sequence. Current algorithms for DCA, although efficient, have a high computational cost of determining Direct Information (DI) values for large proteins or domains. In this paper, we present RADI (Reduced Alphabet Direct Information), a variation of the original DCA algorithm that simplifies the computation of DI values by grouping physicochemically equivalent residues.

Results We have compared the first top ranking 40 pairs of DI values and their closest paired contact in 3D. The ranking is also compared with results obtained using a similar but faster approach based on Mutual Information (MI). When we simplify the number of symbols used to describe a protein sequence to 9, RADI achieves similar results as the original DCA (i.e. with the classical alphabet of 21 symbols), while reducing the computation time around 30-fold on large proteins (with length around 1000 residues) and with higher accuracy than predictions based on MI. Interestingly, the simplification produced by grouping amino acids into only two groups (polar and non-polar) is still representative of the physicochemical nature that characterizes the protein structure, having a relevant and useful predictive value, while the computation time is reduced between 100 and 2500-fold.

Availability RADI is available at https://github.com/structuralbioinformatics/RADI

Contact baldo.oliva{at}upf.edu

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 03, 2018.
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RADI (Reduced Alphabet Direct Information): Improving execution time for direct-coupling analysis
Bernat Anton, Mireia Besalú, Oriol Fornes, Jaume Bonet, Gemma De las Cuevas, Narcís Fernández-Fuentes, Baldo Oliva
bioRxiv 406603; doi: https://doi.org/10.1101/406603
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RADI (Reduced Alphabet Direct Information): Improving execution time for direct-coupling analysis
Bernat Anton, Mireia Besalú, Oriol Fornes, Jaume Bonet, Gemma De las Cuevas, Narcís Fernández-Fuentes, Baldo Oliva
bioRxiv 406603; doi: https://doi.org/10.1101/406603

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