Novel matrix invariants for characterization of changes of proteomics maps

Previous studies on mathematical characterization of proteomics maps by sets of map invariants were based on the construction of a set of distance-related matrices obtained by matrix multiplication of a single matrix by itself. Here we consider an alternative characterization of proteomics maps based on a set of matrices characterizing local features of an embedded zigzag curve over the map. It is shown that novel invariants can well characterize proteomics maps. Advantages of the novel approach are discussed.     

Quantitative molecular similarity analysis (QMSA) methods for property estimation: a comparison of property-based,arbitrary, and tailored similarity spaces

Three classes of arbitrary quantitative molecular similarity analysis (QMSA) methods have been computed using atom pairs, topological indices, and physicochemical properties. Tailored QMSA models have been developed using a selected number of TIs chosen by ridge regression. The methods have been applied to the K-nearest neighbor based estimation of log P of two sets of chemicals. Results show that the property-based and tailored QMSA methods are superior to the arbitrary similarity methods in estimating log P of both sets of chemicals     

Quantitative molecular similarity analysis (QMSA) methods for property estimation: A comparison of property-based,arbitrary, and tailored similarity spaces

Three classes of arbitrary quantitative molecular similarity analysis (QMSA) methods have been computed using atom pairs, topological indices, and physicochemical properties. Tailored QMSA models have been developed using a selected number of TIs chosen by ridge regression. The methods have been applied to the K -nearest neighbor based estimation of log P of two sets of chemicals. Results show that the property-based and tailored QMSA methods are superior to the arbitrary similarity methods in estimating log P of both sets of chemicals     

The photolysis of 2-fluorocyclohexanone in the 313-nm region. The elimination of hydrogen fluoride from vibrationally excited fluorocyclopentane

The gas-phase photolysis of 2-fluorocyclohexanone at 313 nm and 120°C is reported. The primary dissociative step appears to be The 1-fluoropentanediyl species can disproportionate to form the 1- and 5-fluoro-1-pentenes, or cyclize to form vibrationally excited fluorocyclopentane. The latter molecule either undergoes collisional stabilization or decomposes unimolecularly to give cyclopentene and HF. The half-quenching pressure for the latter reaction was 2 torr. The disproportionation-to-combination ratic for the diradical was found to be 1.2. Some brief preliminary experiments on the liquid-phase photolysis of 2-chlorocyclohexanone and 2-fluorocyclohexanone are also described.     

Graphical representation and numerical characterization of H5N1 avian flu neuraminidase gene sequence

The high degree of virulence and potential for development of a pandemic strain of the H5N1 avian flu has resulted in wide interest in characterization of the various genes of the H5N1 virus genome. We have considered for our analysis all 173 available complete sequences, as of February 2006, of the neuraminidase gene, which is the target of the most effective treatment regimen comprising the inhibitors oseltamivir and zanamivir. We have used a 2D graphical representation of the neuraminidase RNA sequences of H5N1 strains to identify a few distinct structural motifs. The H5N1 strains were split into two main classes: strains that were benign to human beings in the years up to 1996 and the period 1999-2002 and strains that were highly pathogenic to humans in the periods 1997 and 2003 to present. Comparisons with earlier H1N1 pandemic and epidemic strains have also been made to understand the current status of the gene. Our findings indicate that the base composition and distribution patterns are significantly different in the two periods, and this may be of interest in studying mutational changes in such viral genes.     

Characterization of Molecular Structures Using Topological Indices

Abstract

The characterization of molecular structure using structural invariants has increased greatly over the last ten years. Specifically, topological indices have become more widely used in the quantification of molecular structure for use in quantitative structure-activity relationship studies, chemical documentation, and molecular similarity studies. The basis, calculation, and utility of topological indices has been examined, with an eye to the specific advantages and problems in their use. In addition, variable clustering and principal component analysis are examinee as two potential solutions to the problem of index intercorrelation.