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visGReMLIN: graph mining-based detection and visualization of conserved motifs at 3D protein-ligand interface at the atomic level.
Ribeiro, Vagner S; Santana, Charles A; Fassio, Alexandre V; Cerqueira, Fabio R; da Silveira, Carlos H; Romanelli, João P R; Patarroyo-Vargas, Adriana; Oliveira, Maria G A; Gonçalves-Almeida, Valdete; Izidoro, Sandro C; de Melo-Minardi, Raquel C; Silveira, Sabrina de A.
Afiliación
  • Ribeiro VS; Department of Computer Science, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil.
  • Santana CA; Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
  • Fassio AV; Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
  • Cerqueira FR; Department of Production Engineering, Universidade Federal Fluminense, Petrópolis, 25650-050, Brazil.
  • da Silveira CH; Department of Computer Engineering, Advanced Campus at Itabira, Universidade Federal de Itajubá, Itabira, 35903-087, Brazil.
  • Romanelli JPR; Department of Computer Engineering, Advanced Campus at Itabira, Universidade Federal de Itajubá, Itabira, 35903-087, Brazil.
  • Patarroyo-Vargas A; Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil.
  • Oliveira MGA; Department of Biochemistry and Molecular Biology, Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil.
  • Gonçalves-Almeida V; Instituto de Biotecnologia aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, 36570-900, Brazil.
  • Izidoro SC; Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
  • de Melo-Minardi RC; Department of Computer Engineering, Advanced Campus at Itabira, Universidade Federal de Itajubá, Itabira, 35903-087, Brazil.
  • Silveira SA; Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil.
BMC Bioinformatics ; 21(Suppl 2): 80, 2020 Mar 11.
Article en En | MEDLINE | ID: mdl-32164574
BACKGROUND: Interactions between proteins and non-proteic small molecule ligands play important roles in the biological processes of living systems. Thus, the development of computational methods to support our understanding of the ligand-receptor recognition process is of fundamental importance since these methods are a major step towards ligand prediction, target identification, lead discovery, and more. This article presents visGReMLIN, a web server that couples a graph mining-based strategy to detect motifs at the protein-ligand interface with an interactive platform to visually explore and interpret these motifs in the context of protein-ligand interfaces. RESULTS: To illustrate the potential of visGReMLIN, we conducted two cases in which our strategy was compared with previous experimentally and computationally determined results. visGReMLIN allowed us to detect patterns previously documented in the literature in a totally visual manner. In addition, we found some motifs that we believe are relevant to protein-ligand interactions in the analyzed datasets. CONCLUSIONS: We aimed to build a visual analytics-oriented web server to detect and visualize common motifs at the protein-ligand interface. visGReMLIN motifs can support users in gaining insights on the key atoms/residues responsible for protein-ligand interactions in a dataset of complexes.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Interfaz Usuario-Computador / Proteínas / Ligandos Tipo de estudio: Diagnostic_studies Límite: Humans Idioma: En Revista: BMC Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2020 Tipo del documento: Article País de afiliación: Brasil Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Interfaz Usuario-Computador / Proteínas / Ligandos Tipo de estudio: Diagnostic_studies Límite: Humans Idioma: En Revista: BMC Bioinformatics Asunto de la revista: INFORMATICA MEDICA Año: 2020 Tipo del documento: Article País de afiliación: Brasil Pais de publicación: Reino Unido