Ensemble approach to predict specificity determinants: benchmarking and validation

<p>Abstract</p> <p>Background</p> <p>It is extremely important and challenging to identify the sites that are responsible for functional specification or diversification in protein families. In this study, a rigorous comparative benchmarking protocol was employed to provide a reliable evaluation of methods which predict the specificity determining sites. Subsequently, three best performing methods were applied to identify new potential specificity determining sites through ensemble approach and common agreement of their prediction results.</p> <p>Results</p> <p>It was shown that the analysis of structural characteristics of predicted specificity determining sites might provide the means to validate their prediction accuracy. For example, we found that for smaller distances it holds true that the more reliable the prediction method is, the closer predicted specificity determining sites are to each other and to the ligand.</p> <p>Conclusion</p> <p>We observed certain similarities of structural features between predicted and actual subsites which might point to their functional relevance. We speculate that majority of the identified potential specificity determining sites might be indirectly involved in specific interactions and could be ideal target for mutagenesis experiments.</p

Single Gene Inheritance Of Occurrence Of Head Spots In Mice

Results from earlier selection studies indicated that while the size of head spots in mice descended from the Goodale head-spot strain was a quantitative, polygenic trait, head-spot occurrence was probably a qualitative trait inherited by one or two genes. The present study was undertaken to examine this possibility by crossing a head-spot stock with three inbred strains and with two noninbred stocks carrying mutant genes. Observed segregation ratios in the F2 and backcross generations of these crosses were compared to results expected under various models of qualitative inheritance. Evidence of linkage between known loci and a putative head-spot gene also was sought. Results indicated that head spotting was inherited primarily by the action of a recessive autosomal gene, head spot (hs). The action of this gene was subject to modification, in some crosses, by other genes or by environmental factors. Attempts to demonstrate linkage between the head spots and known single-locus traits were unsuccessful