PocketMatch: A new algorithm to compare binding sites in protein structures

Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental
requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of
the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the enormous amount of structural data that is being rapidly accumulated, it is essential to have high throughput tools that enable large scale binding site comparison.

Results: Here we present a new algorithm PocketMatch for comparison of binding sites in a frame invariant
manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites. A comprehensive sensitivity analysis and an extensive validation of the algorithm have been carried out. Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. Our analysis also demonstrates that shape information alone is insufficient to discriminate between diverse binding sites, unless
combined with chemical nature of amino acids.

Conclusions: A new algorithm has been developed to compare binding sites in accurate, efficient and
high-throughput manner. Though the representation used is conceptually simplistic, we demonstrate that along
with the new alignment strategy used, it is sufficient to enable binding comparison with high sensitivity. Novel methodology has also been presented for validating the algorithm for accuracy and sensitivity with respect to geometry and chemical nature of the site. The method is also fast and takes about 1/250th second for one comparison on a single processor. A parallel version on BlueGene has also been implemented

Studies on electrode kinetics of schiff bases in aqueous and DMF media

947-950Electrochemical reduction of schiff  bases, viz., salicylidene-2-hydroxyaniline (1), acetophenonidene- 2-hydroxyaniline (2), 4-hydroxyacetophenonidene- 2-hydroxy aniline (3) and 4-hydroxyaceto- phenonidene-2-hydroxy-5-chloroaniline (4) using techniques of cyclic voltammetry, chronoamperometry and chronopotentiometry in buffer solutions of different pH and in 100% DMF at HMDE have been carried out. The kinetic parameters have been determined and the mechanism for electrochemical reduction of these schiff bases has also been proposed

Ruthenium(III) chloride in aqueous solution: effects of temperature, ionic strength and solvent isotope on aquation and anation reactions of the chloro complexes

The kinetics of aquation and anation of [RuCl<SUB>4</SUB>(H<SUB>2</SUB>O)<SUB>2</SUB>]<SUP>−</SUP> (1), [RuCl<SUB>3</SUB>(H<SUB>2</SUB>O)<SUB>3</SUB>] (2), [RuCl<SUB>2</SUB>(H<SUB>2</SUB>O)<SUB>4</SUB>]<SUP>+</SUP> (3) and [RuCl(H<SUB>2</SUB>O)<SUB>5</SUB>]<SUP>2+</SUP> (4) species were studied spectrophotometrically at 288, 298, 308 and 318 K and the activation parameters corresponding to these reactions determined. Effects of ionic strength (0.02-0.2 M KCl) and solvent isotope (k<SUB>H<SUB>2</SUB>O</SUB>/k<SUB>D<SUB>2</SUB>O</SUB>) on aquation and anation processes of 1-4 were investigated at 308 K. The data were interpreted and discussed in support of the mechanistic steps proposed for these reactions. A linear free energy relationship between the thermodynamic data corresponding to the rate steps was also obtained

Electrolytic synthesis of succinic acid in a flow reactor with solid polymer electrolyte membrane

This paper describes the galvanostatic synthesis of succinic acid from maleic acid in an ion exchange membrane flow cell. The electrolysis was carried out at stainless steel, lead and copper cathodes under variable conditions of current density and substrate concentration. Depending upon the experimental conditions, the yield of succinic acid varied from 95 and 99% with a coulombic efficiency of 80–99%. The product was characterized by various physicochemical techniques, viz. 1H-NMR, IR and UV–Visible spectroscopy and elemental analysis. The operational conditions giving maximum yield of product were identified. The mechanism of electrochemical reduction of maleic acid and advantages of using a catholyte without supporting electrolyte are discussed

trans-Dioxo-bis(dimethylglyoximato)ruthenium(VII) perchlorate: an active oxidation catalyst for the electrochemical epoxidation of olefins

High-valent metal-oxo complexes of the composition [Ru<SUP>VI</SUP>(H-dmg)<SUB>2−</SUB> (H<SUB>2</SUB>O)(H)]<SUP>2+</SUP> [Ru<SUP>VII</SUP>(H<SUB>2</SUB>-dmg)<SUB>2</SUB>(OH)(O)<SUP>4+</SUP> where dmg = dimethylglyoximato are formed in situ by the electrochemical oxidation of [Ru<SUP>III</SUP>(H-dmg)<SUB>2−</SUB> (C1O<SUB>4</SUB>)<SUB>2</SUB>]<SUP>−</SUP> in the pH range 1-2 and [Ru<SUP>VI</SUP>(H-dmg)<SUB>2</SUB>(H<SUB>2</SUB>O)(O)]<SUP>2+</SUP> and [Ru<SUP>VII</SUP>-(H-dmg)<SUB>2</SUB>(O)<SUB>2</SUB>]<SUP>+</SUP> in the pH range 2-3.5. These intermediates act as catalysts in the electrocatalytic epoxidation of cyclohexene and cyclooctene to the corresponding epoxides