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Using linear algebra for protein structural comparison and classification Genet. Mol. Biol.
Gomide,Janaína; Melo-Minardi,Raquel; Santos,Marcos Augusto dos; Neshich,Goran; Meira Jr.,Wagner; Lopes,Júlio César; Santoro,Marcelo.
In this article, we describe a novel methodology to extract semantic characteristics from protein structures using linear algebra in order to compose structural signature vectors which may be used efficiently to compare and classify protein structures into fold families. These signatures are built from the pattern of hydrophobic intrachain interactions using Singular Value Decomposition (SVD) and Latent Semantic Indexing (LSI) techniques. Considering proteins as documents and contacts as terms, we have built a retrieval system which is able to find conserved contacts in samples of myoglobin fold family and to retrieve these proteins among proteins of varied folds with precision of up to 80%. The classifier is a web tool available at our laboratory website....
Tipo: Info:eu-repo/semantics/article Palavras-chave: Protein classification; Contact maps; Linear algebra; Singular value decomposition; Latent semantic indexing.
Ano: 2009 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572009000300032
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Mutants of common bean alpha-amylase inhibitor-2 as an approach to investigate binding specificity to alpha-amylases PAB
Silva,Maria Cristina Mattar da; Mello,Luciane Vieira; Coutinho,Marise Ventura; Rigden,Daniel John; Neshich,Goran; Chrispeels,Maarten John; Grossi-de-Sá,Maria Fátima.
Despite the presence of a family of defense proteins, Phaseolus vulgaris can be attacked by bruchid insects resulting in serious damage to stored grains. The two distinct active forms of a-amylase inhibitors, a-AI1 and a-AI2, in P. vulgaris show different specificity toward a-amylases. Zabrotes subfasciatus a-amylase is inhibited by a-AI2 but not by a-AI1. In contrast, porcine a-amylase is inhibited by a-AI1 but not by a-AI2. The objective of this work was to understand the molecular basis of the specificity of two inhibitors in P. vulgaris (a-AI1 and a-AI2) in relation to a-amylases. Mutants of a-AI2 were made and expressed in tobacco plants. The results showed that all the a-AI2 mutant inhibitors lost their activity against the insect a-amylases but none...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Phaseolus vulgaris; A-amylase inhibitors; Inhibitor specificity; Site directed mutagenesis; Structural modeling.
Ano: 2004 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2004000300001
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