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Background: Protein-protein interactions (PPIs) are fundamental in many biological processes and understanding these interactions is key for a myriad of applications including drug development, peptide design and identification of drug targets. The biological data deluge demands efficient and scalable methods to characterize and understand protein-protein interfaces. In this paper, we present ppiGReMLIN, a graph based strategy to infer interaction patterns in a set of protein-protein complexes. Our method combines an unsupervised learning strategy with frequent subgraph mining in order to detect conserved structural arrangements (patterns) based on the physicochemical properties of atoms on protein interfaces. To assess the ability of ppiGReMLIN to point out relevant conserved substructures on protein-protein interfaces, we compared our results to experimentally determined patterns that are key for protein-protein interactions in 2 datasets of complexes, Serine-protease and BCL-2. Results: ppiGReMLIN was able to detect, in an automatic fashion, conserved structural arrangements that represent highly conserved interactions at the specificity binding pocket of trypsin and trypsin-like proteins from Serine-protease dataset. Also, for the BCL-2 dataset, our method pointed out conserved arrangements that include critical residue interactions within the conserved motif LXXXXD, pivotal to the binding specificity of BH3 domains of pro-apoptotic BCL-2 proteins towards apoptotic suppressors. Quantitatively, ppiGReMLIN was able to find all of the most relevant residues described in literature for our datasets, showing precision of at least 69% up to 100% and recall of 100%. Conclusions: ppiGReMLIN was able to find highly conserved structures on the interfaces of protein-protein complexes, with minimum support value of 60%, in datasets of similar proteins. We showed that the patterns automatically detected on protein interfaces by our method are in agreement with interaction patterns described in the literature.
Este artículo de investigación presenta resultados de un estudio sobre las prácticas usadas por los colegios de Bogotá para enfrentar los riesgos de agresión (física y verbal) y consumo de sustancias (alcohol, cigarrillo y drogas). En la investigación se usaron datos cuantitativos de una encuesta representativa a colegios de la ciudad y datos cualitativos de grupos focales con docentes y directivos docentes. Consideramos cuatro tipos de estrategias: punitivas, normativas, pedagógicas y espaciales. Se encuentra que, para el caso de la agresión, los cuatro tipos de estrategias son usadas. Los rectores reportan un mayor uso de estrategias pedagógicas y normativas que punitivas o espaciales, pero los docentes reportan un uso muy similar de las cuatro estrategias. Los resultados cualitativos se usan para discutir alternativas de política, la clasificación de estrategias y cómo, en muchos casos, esta clasificación tiene matices.
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