DockYard-a repository to assist modeling of protein-protein docking

In the absence of interlogs, building docking models is a time intensive task, involving generation of a large pool of docking decoys followed by refinement and screening to identify near native docking solutions. This limits the researcher interested in building docking methods with the choice of benchmarking only a limited number of protein complexes. We have created a repository called dockYard (http://pallab.serc.iisc.ernet.in/dockYard), that allows modelers interested in protein-protein interaction to access large volume of information on protein dimers and their interlogs, and also download decoys for their work if they are interested in building modeling methods. dockYard currently offers four categories of docking decoys derived from: Bound (native dimer co-crystallized), Unbound (individual subunits are crystallized, as well as the target dimer), Variants (match the previous two categories in at least one subunit with 100% sequence identity), and Interlogs (match the previous categories in at least one subunit with >= 90% or >= 50% sequence identity). The web service offers options for full or selective download based on search parameters. Our portal also serves as a repository to modelers who may want to share their decoy sets with the community.

Modeling of a reacting nanofilm on a composite substrate

This article provides a detailed computational analysis of the reaction of dense nanofilms and the heat transfer characteristics on a composite substrate. Although traditional energetic compounds based on organic materials have similar energy per unit weight, non-organic material in nanofilm configuration offers much higher energy density and higher flame speed. The reaction of a multilayer thin film of aluminum and copper oxide has been studied by varying the substrate material and thicknesses. The numerical analysis of the thermal transport of the reacting film deposited on the substrate combined a hybrid approach in which a traditional two-dimensional black box theory was used in conjunction with the sandwich model to estimate the appropriate heat flux on the substrate accounting for the heat loss to the surroundings. A procedure to estimate this heat flux using stoichiometric calculations is provided. This work highlights two important findings. One is that there is very little difference in the temperature profiles between a single substrate of silica and a composite substrate of silicon silica. Secondly, with increase in substrate thickness, the quenching effect is progressively diminished at a given speed. These findings show that the composite substrate is effective and that the average speed and quenching of flames depend on the thickness of the silica substrate, and can be controlled by a careful choice of the substrate configuration. (C) 2011 Elsevier Ltd. All rights reserved.

Sibling rivalry between seeds within a fruit: Some population genetic models

Competition between seeds within a fruit for parental resources is described using one-locus-two-allele models. While a �normal� allele leads to an equitable distribution of resources between seeds (a situation which also corresponds to the parental optimum), the �selfish� allele is assumed to cause the seed carrying it to usurp a higher proportion of the resources. The outcome of competition between �selfish� alleles is also assumed to lead to an asymmetric distribution of resources, the �winner� being chosen randomly. Conditions for the spread of an initially rare selfish allele and the optimal resource allocation corresponding to the evolutionarily stable strategy, derived for species with n-seeded fruits, are in accordance with expectations based on Hamilton�s inclusive fitness criteria. Competition between seeds is seen to be most intense when there are only two seeds, and decreases with increasing number of seeds, suggesting that two-seeded fruits would be rarer than one-seeded or many-seeded ones. Available data from a large number of plant species are consistent with this prediction of the model.

The structures of bacteriorhodopsin with different retinal-Schiff base orientations--computer modeling and energy minimization studies

Bacteriorhodopsin has been the subject of intense study in order to understand its photochemical function. The recent atomic model proposed by Henderson and coworkers based on electron cryo-microscopic studies has helped in understanding many of the structural and functional aspects of bacteriorhodopsin. However, the accuracy of the positions of the side chains is not very high since the model is based on low-resolution data. In this study, we have minimized the energy of this structure of bacteriorhodopsin and analyzed various types of interactions such as - intrahelical and interhelical hydrogen bonds and retinal environment. In order to understand the photochemical action, it is necessary to obtain information on the structures adopted at the intermediate states. In this direction, we have generated some intermediate structures taking into account certain experimental data, by computer modeling studies. Various isomers of retinal with 13-cis and/or 15-cis conformations and all possible staggered orientations of Lys-216 side chain were generated. The resultant structures were examined for the distance between Lys-216-schiff base nitrogen and the carboxylate oxygen atoms of Asp-96 - a residue which is known to reprotonate the schiff base at later stages of photocycle. Some of the structures were selected on the basis of suitable retinal orientation and the stability of these structures were tested by energy minimization studies. Further, the minimized structures are analyzed for the hydrogen bond interactions and retinal environment and the results are compared with those of the minimized rest state structure. The importance of functional groups in stabilizing the structure of bacteriorhodopsin and in participating dynamically during the photocycle have been discussed.

Water Modeling Study Of The Jet Characteristics In A Continuous-Casting Mold

The jet characteristics and the fluid flow pattern in a continuous slab caster have been studied using a water model. The fluid jet is studied under free fall and submerged discharge conditions. In the latter case, the jet was followed by dye-injection technique and image analyser was used to find out the effect of nozzle parameters on jet-spread angle, jet-discharge angle and the volume entrainment by the jet. All free-fall jets with nozzle port angle zero and upward are found to be spinning. Some of the free-fall jets with downward nozzle-port angle are found to be spinning and rest are smooth. The spinning direction of the jets are found to change with time. The well depth, port diameter and the inner diameter of the nozzle have a clear effect on the free-fall jets with downward port angle. The jet-spread angle is found to be about 17-degrees for smooth jets. The spread angle for spinning jet increases as the nozzle-port angle is increased from downward 25 to upward 15-degrees. The jet-discharge angle is always downward even when the nozzle-discharge ports are angled upward. The extent of volume entrainment by the spinning jet is higher and it increases as the nozzle-port angle is increased from 25 downward to 15-degrees upward.