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GAPIN: Grouped and Aligned Protein Interface Networks

Biharck M. Araújo, Aline L. Coelho, Sabrina A. Silveira, João P. R. Romanelli, Raquel C. de Melo-Minardi, Carlos H. da Silveira
doi: https://doi.org/10.1101/520833
Biharck M. Araújo
1Bioinformatics PhD Program, Universidade Federal de Minas Gerais, 31270-901, Brazil
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Aline L. Coelho
2School of Medicine - EMED / Universidade Federal de Ouro Preto, 35400-000, Brazil
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Sabrina A. Silveira
1Bioinformatics PhD Program, Universidade Federal de Minas Gerais, 31270-901, Brazil
3Department of Computer Science, Universidade Federal de Viçosa, 36570-900, Brazil
4European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
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João P. R. Romanelli
5Institute of Applied and Pure Sciences, Universidade Federal de Itajubá, 35903-087, Brazil
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Raquel C. de Melo-Minardi
1Bioinformatics PhD Program, Universidade Federal de Minas Gerais, 31270-901, Brazil
6Department of Computer Science, Universidade Federal de Minas Gerais, 31270-901, Brazil
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Carlos H. da Silveira
1Bioinformatics PhD Program, Universidade Federal de Minas Gerais, 31270-901, Brazil
6Department of Computer Science, Universidade Federal de Minas Gerais, 31270-901, Brazil
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Abstract

Summary GAPIN is a web-based application for structural interaction network analysis among any type of PDB molecules, regardless of whether their interfaces are between chain-chain or chain-ligand. A special emphasis is given to graph clustering, allowing users to scrutinize target contexts for ligand candidates. We show how GAPIN can be used to unveil underlying hydrophobic patterns on a set of peptidase-inhibitor complexes. In another experiment, we show there is a positive correlation between cluster sizes and the presence of druggable spots, indicating that the clustering may discriminate the higher complexity of these hot subnetworks.

Availability and implementation GAPIN is freely available as an easy-to-use web interface available at https://pinga.unifei.edu.br.

Contact biharck{at}ufmg.br, carlos.silveira{at}unifei.edu.br.

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 March 04, 2019.
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GAPIN: Grouped and Aligned Protein Interface Networks
Biharck M. Araújo, Aline L. Coelho, Sabrina A. Silveira, João P. R. Romanelli, Raquel C. de Melo-Minardi, Carlos H. da Silveira
bioRxiv 520833; doi: https://doi.org/10.1101/520833
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GAPIN: Grouped and Aligned Protein Interface Networks
Biharck M. Araújo, Aline L. Coelho, Sabrina A. Silveira, João P. R. Romanelli, Raquel C. de Melo-Minardi, Carlos H. da Silveira
bioRxiv 520833; doi: https://doi.org/10.1101/520833

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