Consensus scoring for enriching near-native structures from protein-protein docking decoys

The identification of near native protein-protein complexes among a set of decoys remains highly challenging. A stategy for improving the success rate of near native detection is to enrich near native docking decoys in a small number of top ranked decoys. Recently, we found that a combination of three scoring functions (energy, conservation, and interface propensity) can predict the location of binding interface regions with reasonable accuracy. Here, these three scoring functions are modified and combined into a consensus scoring function called ENDES for enriching near native docking decoys. We found that all individual scores result in enrichment for the majority of 28 targets in ZDOCK2.3 decoy set and the 22 targets in Benchmark 2.0. Among the three scores, the interface propensity score yields the highest enrichment in both sets of protein complexes. When these scores are combined into the ENDES consensus score, a significant increase in enrichment of near-native structures is found. For example, when 2000 dock decoys are reduced to 200 decoys by ENDES, the fraction of near-native structures in docking decoys increases by a factor of about six in average. ENDES was implemented into a computer program that is available for download at http://sparks.informatics.iupui.edu.

Effects of spark discharge on the anodic coatings on magnesium alloy

Spark discharge was the representative phenomenon of Micro-arc oxidation (MAO) method distinguished from other electrochemical oxidation methods. Under the spark discharge treatment, characteristics of the anodic layer were significantly changed. To investigate the influences of the spark discharge, a piece of magnesium alloy AZ91D specimen was partly treated by MAO method in alkaline silicate solution. And the microstructure, element distributions as well as the surface potential distributions of the specimen were studied by scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS) and scanning Kelvin probe (SKP) technique. As a result of intensive spark discharge treatment, porous external layer with dense internal layer were formed on Mg alloy surface. At the same time, the depositions of OH- and SiO32- ions were accelerated, which resulted in the enrichment of element oxygen and silicon at the spark discharge region. Moreover, due to the compact internal layer, the intensive spark discharge region exhibited more positive potentials with respect to other regions, which meant this region could restrain the ejection of electron and provide effective protection to the substrate. In addition, it was found that oxygen played a vital role in determining the intensity and size of sparks, and abundant oxygen resulted in intensive and larger sparks. (c) 2005 Elsevier B.V. All rights reserved.