Using linear algebra for protein structural comparison and classification.

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. Users can search for similar chains from a specific PDB, view and compare their contact maps and browse their structures using a JMol plug-in.

Electrochemical and quantum chemical investigations of the insecticide fipronil.

This work describes an electrochemical and quantum chemical investigation of the fipronil insecticide. Cyclic voltammetry (CV) and square wave voltammetry (SWV) experiments were performed over a graphite-polyurethane (GPU) composite electrode. The fipronil molecule presents an one?electron irreversible oxidation reaction. Profiting the SWV signal a square wave stripping voltammetry (SWSV) procedure to determine the fipronil molecule in a 0.10 mol L-1 Britton-Robinson buffer solution, pH 8.0 was developed with accumulation potential and time of 0.50 V and 120 s, respectively. The limits of detection and quantification were 0.80 and 2.67 ?g L-1, respectively. Recovery tests were performed in three natural waters samples with values ranging from 99.67 to 101.37%. Quantum chemical studies showed that the nitrogen atom of the pyrazole group is the most probable oxidation site of the fipronil molecule.