J Integr Bioinform - Predicting protein distance maps according to physicochemical properties.

Tópicos

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{ model(2656) set(1616) predict(1553) }
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Resumo

The prediction of protein structures is a current issue of great significance in structural bioinformatics. More specifically, the prediction of the tertiary structure of a protein consists in determining its three-dimensional conformation based solely on its amino acid sequence. This study proposes a method in which protein fragments are assembled according to their physicochemical similarities, using information extracted from known protein structures. Many approaches cited in the literature use the physicochemical properties of amino acids, generally hydrophobicity, polarity and charge, to predict structure. In our method, implemented with parallel multithreading, we used a set of 30 physicochemical amino acid properties selected from the AAindex database. Several protein tertiary structure prediction methods produce a contact map. Our proposed method produces a distance map, which provides more information about the structure of a protein than a contact map. We performed several preliminary analysis of the protein physicochemical data distributions using 3D surfaces. Three main pattern types were found in 3D surfaces, thus it is possible to extract rules in order to predict distances between amino acids according to their physicochemical properties. We performed an experimental validation of our method using five non-homologous protein sets and we showed the generality of this method and its prediction quality using the amino acid properties considered. Finally, we included a study of the algorithm efficiency according to the number of most similar fragments considered and we notably improved the precision with the studied proteins sets.

Resumo Limpo

predict protein structur current issu great signific structur bioinformat specif predict tertiari structur protein consist determin threedimension conform base sole amino acid sequenc studi propos method protein fragment assembl accord physicochem similar use inform extract known protein structur mani approach cite literatur use physicochem properti amino acid general hydrophob polar charg predict structur method implement parallel multithread use set physicochem amino acid properti select aaindex databas sever protein tertiari structur predict method produc contact map propos method produc distanc map provid inform structur protein contact map perform sever preliminari analysi protein physicochem data distribut use d surfac three main pattern type found d surfac thus possibl extract rule order predict distanc amino acid accord physicochem properti perform experiment valid method use five nonhomolog protein set show general method predict qualiti use amino acid properti consid final includ studi algorithm effici accord number similar fragment consid notabl improv precis studi protein set

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