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

Performance of layers on sorghum-based poultry feed rations

In this study, Sorghum bicolor cultivars CSV 15, PSV 16, CSH 16 and S 35 were supplied to farmers in Mahabubnagar and Ranga Reddy districts in Andhra Pradesh, India, in 2003 for poultry feed trials. Sorghum replaced maize at 0, 50 and 100% levels, including a 100% replacement + 3% Stylosanthes (Stylo) of the control diet. 500 chicks were divided into 42 groups with 6 treatments at 0, 50 and 100% sorghum diets in mash and pelleted forms

Performance of broilers on sorghum-based diets

The effect of replacing maize with sorghum grain on the performance of broilers was studied. Grain from 4 improved Sorghum bicolor cultivars (CSH 16, CSV 15, PSV 16 and S 35) and one traditional yellow variety were used to replace maize (control diet) in the starter (1-4 weeks) and finisher rations (5-6 weeks) of broilers by 50, 75 and 100% levels. All diets were isonitrogenous and isocaloric and were homogeneous for lysine, methionine and cystine levels. One-day-old 512 commercial Cobb female broilers were divided into 64 groups with 16 dietary treatments and 4 replicates per treatment, with 8 birds in each. In a second trial, sorghum replacement was conducted without homogenizing the diets for nitrogen and energy contents. The study lasted for 6 weeks. It was shown that the liveweight gain and feed intake of broilers was statistically similar in sorghum diets at all inclusion levels compared to the control diet. However, the feed conversion efficiency of broilers in the 100% sorghum diet was significantly higher compared to the maize diet (P=0.05). A better feed conversion efficiency was found with the CSV 15, CSH 16, PSV 16 and the local cultivars at 100% inclusion levels. However, the yellow pigmentation of the skin and carcass of the broilers was better in the maize diet compared to the sorghum diets. Cost varied among and within cultivars at different inclusion levels, and was lower in CSV 15, PSV 16, S 35 and local sorghum cultivar-based diets. Cost was also much lower in CSV 15, PSV 16 and local sorghum cultivars at 100% inclusion level compared to maize. Feed cost per kg liveweight gain was lower with CSV 15 (Rs 17.16) and PSV 16 cultivars (Rs 17.62) compared to maize (Rs 18.02). Although pelleting increased feed costs (by Rs 0.25/kg), it also improved broiler production efficiency compared to mash in sorghum diets. Inclusion of Stylosanthes sp. leaf meal at 3% in 100% sorghum-based diets favourably improved the shank and skin colour of the carcass. Carcass yield and abdominal fat of broilers fed sorghum, sorghum + Stylosanthes sp. and maize diets were similar. In conclusion, the inclusion/replacement of sorghum in maize-based diets and pelleting improves the feed conversion ratio and decreases the total feed costs in broiler production

Polarographic & Potentiometric Study of Ru(III)-EDTA Complexes

441-44

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

Kinetic and electrochemical aspects of two-electron reduction of ferrofluid by vitamin C in dilute aqueous solution

350-355<span style="font-size:11.0pt;line-height:115%; font-family:" calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-fareast-font-family:="" "times="" new="" roman";mso-fareast-theme-font:minor-fareast;mso-hansi-theme-font:="" minor-latin;mso-bidi-font-family:arial;mso-ansi-language:en-us;mso-fareast-language:="" en-us;mso-bidi-language:ar-sa"="">The two-electron reduction of ferrofluid (FF) by vitamin C (L-ascorbic acid, H2A) and the reoxidation of the reduced product by molecular oxygen has been investigated in dilute aqueous acidic solutions (<i style="mso-bidi-font-style: normal">pH 2.5 -4.0) as a function of the variants, temperature ionic strength and concentrations of FF, H2A, H+ and molecular oxygen using potentiometric, spectrophotometric and voltammetric techniques. The rate of reaction was found to be first order with respect to the concentrations of H2A and FF, zero order with respect to molecular oxygen, inverse first order with respect to H+ and independent of ionic strength. The experimental results are interpreted in terms of a mechanism involving a rate determining outer sphere one-electron transfer. from vitamin C to FF followed by a subsequent and kinetically rapid transfer of the second electron of vitamin C to the same molecule of FF, which was already reduced by one electron in the rate determining step. Reduced product of FF gets reoxidized by molecular oxygen, making the overall two-electron oxidation of H2A catalytic at appreciable lower thermodynamic quantities.</span

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