RESUMO
MOTIVATION: The large variety of antimicrobial peptide (AMP) databases developed to date are characterized by a substantial overlap of data and similarity of sequences. Our goals are to analyze the levels of redundancy for all available AMP databases and use this information to build a new non-redundant sequence database. For this purpose, a new software tool is introduced. RESULTS: A comparative study of 25 AMP databases reveals the overlap and diversity among them and the internal diversity within each database. The overlap analysis shows that only one database (Peptaibol) contains exclusive data, not present in any other, whereas all sequences in the LAMP_Patent database are included in CAMP_Patent. However, the majority of databases have their own set of unique sequences, as well as some overlap with other databases. The complete set of non-duplicate sequences comprises 16 990 cases, which is almost half of the total number of reported peptides. On the other hand, the diversity analysis identifies the most and least diverse databases and proves that all databases exhibit some level of redundancy. Finally, we present a new parallel-free software, named Dover Analyzer, developed to compute the overlap and diversity between any number of databases and compile a set of non-redundant sequences. These results are useful for selecting or building a suitable representative set of AMPs, according to specific needs.
Assuntos
Peptídeos Catiônicos Antimicrobianos/química , Bases de Dados de Ácidos Nucleicos , Bases de Dados de Proteínas , Análise de Sequência de Proteína/métodos , Software , Algoritmos , HumanosRESUMO
The principles governing protein folding stand as one of the biggest challenges of Biophysics. Modeling the global stability of proteins and predicting their tertiary structure are hard tasks, due in part to the variety and large number of forces involved and the difficulties to describe them with sufficient accuracy. We have developed a fast, physics-based empirical potential, intended to be used in global structure prediction methods. This model considers four main contributions: Two entropic factors, the hydrophobic effect and configurational entropy, and two terms resulting from a decomposition of close-packing interactions, namely the balance of the dispersive interactions of folded and unfolded states and electrostatic interactions between residues. The parameters of the model were fixed from a protein data set whose unfolding free energy has been measured at the "standard" experimental conditions proposed by Maxwell et al. (2005) and a large data set of 1151 monomeric proteins obtained from the PDB. A blind test with proteins taken from ProTherm database, at similar experimental conditions, was carried out. We found a good correlation with the test data set, proving the effectiveness of our model for predicting protein folding free energies in considered standard conditions. Such a prediction compares favorably against estimations made with FoldX's function and the force field GROMOS96. This model constitutes a valuable tool for the fast evaluation of protein structure stability in 3D structure prediction methods.
Assuntos
Dobramento de Proteína , Proteínas/química , Algoritmos , Bases de Dados de Proteínas , Modelos Lineares , Modelos Estatísticos , Estrutura Terciária de Proteína , Reprodutibilidade dos Testes , Software , TermodinâmicaRESUMO
La presente investigación describe el control y seguimiento que el Programa Fluoruración de la Sal Doméstica de Costa Rica realiza a nivel nacional en las salineras y en los expendios al público para velar porque se cumplan las normas para la sal de consumo doméstico. La norma para la sal de consumo doméstico en Costa Rica estipula que el contenido de flúor debe ser de 225 a 275 ppm y el de yodo debe ser de 33 a 50 ppm. Se realizaron dos tipo de controles para lograr la verificación del cumplimiento de la norma: un control interno realizado por parte de las salineras que participan en el Programa y un control externo que se realiza en el Laboratorio de bromatología del INCIENSA. Se utilizó la técnica del electrodo de ión específico para las mediciones de flúor y yodo en la sal que se produce para el consumo humano. Los resultados obtenidos durante dos años y nueve meses desde la incorporación de la doble fortificación (flúor-yodo) de la sal muestran que el contenido promedio de flúor en la sal fue de: 237 ppm en COONAPROSAL, 224 ppm en COOPEPROSA y de 237 ppm en la EMPACADORA SAL DIAMANTE. Los valores promedio de yodo para el período en estudio fueron: 39 ppm en COONAPROSAL, 27 ppm en COOPEPROSA y 33 ppm en la EMPACADORA SAL DIAMANTE. Se concluye que el proceso de la fluoruración de la sal es un proceso controlado en las tres salineras analizadas y que la efectividad de un programa como el descrito requiere de estudios de control y seguimiento