LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites

We present a new shape-based method, LigandFit, for accurately docking ligands into protein active sites. The method employs a cavity detection algorithm for detecting invaginations in the protein as candidate active site regions. A shape comparison filter is combined with a Monte Carlo conformational search for generating ligand poses consistent with the active site shape. Candidate poses are minimized in the context of the active site using a grid-based method for evaluating protein-ligand interaction energies. Errors arising from grid interpolation are dramatically reduced using a new non-linear interpolation scheme. Results are presented for 19 diverse protein-ligand complexes. The method appears quite promising, reproducing the X-ray structure ligand pose within an RMS of 2A in 14 out of the 19 complexes. A high-throughput screening study applied to the thymidine kinase receptor is also presented in which LigandFit, when combined with LigScore, an internally developed scoring function, yields very good hit rates for a ligand pool seeded with known actives.     

Composition, structural, dielectric and DC characterization of vacuum deposited ZnSe thin films

ZnSe thin films with different thicknesses are deposited onto glass substrates under a vacuum of 4×10⁻⁵ mbar by vacuum evaporation. Rutherford backscattering spectrometry is used to identify the composition of the deposited films. The composition of the deposited films is found to be nearly stoichiometric. The X-ray diffractogram reveals a cubic structure with preferential orientation along the (1 1 1) direction and structural parameters such as crystallite size D, dislocation density δ, strain ε, and lattice parameters are calculated. It is observed that the crystallite size increases from 20.11 to 55.56 nm with increase of film thickness. In the DC conduction studies the conduction mechanism is found to follow an exponential trap distribution with density of states 3.251×10⁴⁸ J⁻¹ m⁻³. The dielectric constant is calculated as 8.11 [306 K].     

Experimental Analysis of Flexibility Change with Different Levels of Power Reduction by Demand Response Activation on Thermostatically Controlled Loads

This paper studies the flexibility available with thermostatically controlled loads (TCLs) to provide power system services by demand response (DR) activation. Although the DR activation on TCLs can provide power system ancillary services, it is important to know how long such services can be provided for when different levels of power reduction are imposed. The flexibility change with different levels of power reduction is tested experimentally with domestic fridges used by real customers with unknown user interaction. The investigation quantifies the flexibility of household fridges and the impact of DR activation in terms of deviation in the average temperature. The maximum possible power reduction with the cluster of refrigerators is 67% and the available flexibility with the cluster of refrigerators is 10%. The resulting deviation in the average temperature is 14%.     

Mechanism of inhibition of electrode reactions at high surface coverages—II

The inhibition of Cu²⁺, Cd²⁺ and Zn²⁺ discharge reactions was studied in the presence of C₄–C₆ alcohols, phenol, benzyl alcohol and cyclohexanol (SAS) in 0.5 M Na₂SO₄ + 1 mM H₂SO₄ supporting electrolyte. It is found from the results that at high surface coverages by SAS, the inhibition is due to “sieve effect” which is different from that at low coverages. The true standard rate constant is proportional to exp[(? N ΔγA_i)/(RT)] where ΔγA_i is the extra energy (in the form of work) that must be done in order to create a free area required for a discharge reaction.     

Investigations on electron beam evaporated Cu(In0.85Ga0.15)Se2 thin film solar cells

CIGS bulk with composition of CuIn_0.85Ga_0.15Se₂ was synthesized by direct reaction of elemental copper, indium, gallium and selenium. CIGS thin films were then deposited onto well-cleaned glass substrates using the prepared bulk alloy by electron beam deposition method. The structural properties of the deposited films were studied using X-ray diffraction technique. The as-deposited CIGS films were found to be amorphous. On annealing, the films crystallized with a tetragonal chalcopyrite structure. An intermediate Cu-rich phase precipitated at 200 °C and dissociated at higher annealing temperatures. Average grain size calculated from the XRD spectra indicated that the films had a nano-crystalline structure and was further corroborated by AFM analysis of the sample surface. The chemical constituents present in the deposited CIGS films were identified using energy dispersive X-ray analysis. CIGS based solar cells were then fabricated on molybdenum and ITO coated glass substrates and the efficiencies have been evaluated.     

Production of Al2O3‐Stabilized Tetragonal ZrO2 Nanoparticles for Thermal Barrier Coating

Al₂O₃‐stabilized tetragonal ZrO₂ nanoparticles were obtained through hot‐air spray pyrolysis and characterized after postsynthesized treatments. The produced nanoparticles were 26 nm in size with surface area of 59 m²/g. A multilayer thermal barrier coating of nanostructured Al₂O₃‐ZrO₂‐embedded silicate was applied to the mild steel (EN3) specimen using spin‐coating technique and characterized comprehensively employing X‐ray diffraction and scanning electron microscope. The Al₂O₃‐stabilized ZrO₂ with silicate matrix facilitates the formation of zirconium silicate nanostructured surface‐protective coating on EN3 specimen. The Al₂O₃‐ZrO₂/SiO₂ matrix‐based hybrid inorganic coating shows effective thermal barrier for EN3 after firing at a high temperature of 600°C.     

Biotic elicitors enhance flavour compounds during accelerated curing of vanilla beans

Food-grade elicitors, selected after an initial screening, were used in combination with pre-treatments for the accelerated curing of beans. When acetone dried red beet elicitor – a rich source of peroxidase (98,500 U g⁻¹ dry weight) was used, 2.65% vanillin was formed in 10 days, which was 1.7-fold higher than in control beans (blanched + scarified) of this study and 3.23-fold higher than the conventional curing (0.82%). HPLC analysis of elicitor-treated samples showed the formation of almost all the major compounds found in the conventionally cured beans (cured for 3–6 months) with better sensorial properties. These observations appear useful for developing a rapid process for the curing of vanilla beans.     

Surface properties of electrodeposited a-Si:C:H:F thin films by X-ray photoelectron spectroscopy

Surface properties of amorphous silicon thin films containing hydrogen, flourine and carbon obtained from hydrofluosilicic acid and ethylene glycol using the electrodeposition method are reported as a function of current density and deposition time. The Si2p core level X-ray photoelectron spectra exhibited binding-energy shifts corresponding to SiFx (x=1–4), SiC, Si-H and Si-O2 type bond formations. The shifts in 1s spectra of fluorine, carbon and oxygen confirmed the presence of fluorine, carbon and oxygen in bonded form. Theoretical binding-energy shifts calculated from Pauling's electronegativity values were in close agreement with the measured values. The relative concentration values of C/Si estimated in these films were found to be larger than those of F/Si and O/Si. The results were corroborated with infrared spectroscopy and scanning electron microscopy data. This revised version was published online in November 2006 with corrections to the Cover Date.