Sequence-based identification of interface residues by an integrative profile combining hydrophobic and evolutionary information

<p>Abstract</p> <p>Background</p> <p>Protein-protein interactions play essential roles in protein function determination and drug design. Numerous methods have been proposed to recognize their interaction sites, however, only a small proportion of protein complexes have been successfully resolved due to the high cost. Therefore, it is important to improve the performance for predicting protein interaction sites based on primary sequence alone.</p> <p>Results</p> <p>We propose a new idea to construct an integrative profile for each residue in a protein by combining its hydrophobic and evolutionary information. A support vector machine (SVM) ensemble is then developed, where SVMs train on different pairs of positive (interface sites) and negative (non-interface sites) subsets. The subsets having roughly the same sizes are grouped in the order of accessible surface area change before and after complexation. A self-organizing map (SOM) technique is applied to group similar input vectors to make more accurate the identification of interface residues. An ensemble of ten-SVMs achieves an MCC improvement by around 8% and F1 improvement by around 9% over that of three-SVMs. As expected, SVM ensembles constantly perform better than individual SVMs. In addition, the model by the integrative profiles outperforms that based on the sequence profile or the hydropathy scale alone. As our method uses a small number of features to encode the input vectors, our model is simpler, faster and more accurate than the existing methods.</p> <p>Conclusions</p> <p>The integrative profile by combining hydrophobic and evolutionary information contributes most to the protein-protein interaction prediction. Results show that evolutionary context of residue with respect to hydrophobicity makes better the identification of protein interface residues. In addition, the ensemble of SVM classifiers improves the prediction performance.</p> <p>Availability</p> <p>Datasets and software are available at <url>http://mail.ustc.edu.cn/~bigeagle/BMCBioinfo2010/index.htm</url>.</p

Elaboration and Validation of the Medication Prescription Safety Checklist

Objetivo: elaborar e validar um instrumento tipo checklist para identificar a adesão às recomendações na estrutura das prescrições de medicamentos, a partir do Protocolo do Ministério da Saúde e Agência Nacional de Vigilância Sanitária. Método: pesquisa metodológica, conduzida por meio do processo de validade e análise de confiabilidade, com amostra de 27 prescrições eletrônicas. Resultados: análises realizadas confirmaram a validade de conteúdo e a confiabilidade da versão do instrumento. A validade de conteúdo, obtida por meio da avaliação de juízes, foi considerada satisfatória por contemplar itens que representam a adesão às recomendações na estrutura das prescrições de medicamentos. A confiabilidade, avaliada por interobservadores, apresentou-se excelente (ICC=1,00) e de concordância perfeita (K=1,00). Conclusão: o instrumento Lista de Verificação de Segurança na Prescrição de Medicamentos demonstrou-se válido e confiável para o grupo estudado. Espera-se que este estudo possa contribuir para a prevenção de eventos adversos, bem como para a melhoria da qualidade da assistência e segurança no uso de medicamentos.Objetivo: elaborar y validar un instrumento tipo checklist para identificar la adhesión a las recomendaciones en la estructura de las prescripciones de medicamentos, a partir del Protocolo del Ministerio de la Salud y Agencia Nacional de Vigilancia Sanitaria. Método: investigación metodológica, conducida mediante el proceso de validez y análisis de confiabilidad, con muestra de 27 prescripciones electrónicas. Resultados: los análisis llevados a cabo confirmaron la validez de contenido y la confiabilidad de la versión del instrumento. La validez de contenido, alcanzada mediante la evaluación de jueces, fue considerada satisfactoria por contemplar ítems que representan la adhesión a las recomendaciones en la estructura de las prescripciones de medicamentos. La confiabilidad, evaluada por interobservadores, se reveló excelente (ICC=1,00) y de concordancia perfecta (K=1,00). Conclusión: el instrumento Lista de Verificación de Seguridad en la Prescripción de Medicamentos se mostró válido y confiable para el grupo estudiado. Se espera que este estudio pueda contribuir hacia la prevención de eventos adversos, y también hacia la mejora de la calidad de la atención y seguridad en el uso de medicamentos.Objective: to elaborate and validate a checklist to identify compliance with the recommendations for the structure of medication prescriptions, based on the Protocol of the Ministry of Health and the Brazilian Health Surveillance Agency. Method: methodological research, conducted through the validation and reliability analysis process, using a sample of 27 electronic prescriptions. Results: the analyses confirmed the content validity and reliability of the tool. The content validity, obtained by expert assessment, was considered satisfactory as it covered items that represent the compliance with the recommendations regarding the structure of the medication prescriptions. The reliability, assessed through interrater agreement, was excellent (ICC=1.00) and showed perfect agreement (K=1.00). Conclusion: the Medication Prescription Safety Checklist showed to be a valid and reliable tool for the group studied. We hope that this study can contribute to the prevention of adverse events, as well as to the improvement of care quality and safety in medication use