visGReMLIN: graph mining-based detection and visualization of conserved motifs at 3D protein-ligand interface at the atomic level

Autor:	Adriana M Patarroyo-Vargas, Fabio Ribeiro Cerqueira, Sabrina de A. Silveira, Raquel C. de Melo-Minardi, Charles A. Santana, Vagner S. Ribeiro, Maria Goreti de Almeida Oliveira, Sandro Carvalho Izidoro, João P. R. Romanelli, Carlos H. da Silveira, Valdete M. Gonçalves-Almeida, Alexandre V. Fassio
Jazyk:	angličtina
Rok vydání:	2020
Předmět:	Web server Computer science 0206 medical engineering 02 engineering and technology Computational biology computer.software_genre Ligands lcsh:Computer applications to medicine. Medical informatics Biochemistry 03 medical and health sciences User-Computer Interface Structural Biology Humans Molecular Biology lcsh:QH301-705.5 030304 developmental biology 0303 health sciences Ligand Applied Mathematics Research Proteins Hydrogen Bonding Small molecule Computer Science Applications Visualization lcsh:Biology (General) Graph (abstract data type) lcsh:R858-859.7 DNA microarray computer Hydrophobic and Hydrophilic Interactions 020602 bioinformatics Protein ligand Protein Binding
Zdroj:	BMC Bioinformatics, Vol 21, Iss S2, Pp 1-12 (2020) BMC Bioinformatics
ISSN:	1471-2105
DOI:	10.1186/s12859-020-3347-7
Popis:	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.
Databáze:	OpenAIRE
Externí odkaz:	https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c76ec61861c41832cab166fb94d1737e http://link.springer.com/article/10.1186/s12859-020-3347-7 Zobrazit plný text záznamu Plný text ve formátu PDF Plný text ve formátu HTML
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