38 research outputs found

    Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures

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    BACKGROUND: Protein-protein interactions (PPIs) mediate the vast majority of biological processes, therefore, significant efforts have been directed to investigate PPIs to fully comprehend cellular functions. Predicting complex structures is critical to reveal molecular mechanisms by which proteins operate. Despite recent advances in the development of new methods to model macromolecular assemblies, most current methodologies are designed to work with experimentally determined protein structures. However, because only computer-generated models are available for a large number of proteins in a given genome, computational tools should tolerate structural inaccuracies in order to perform the genome-wide modeling of PPIs. RESULTS: To address this problem, we developed eRank(PPI), an algorithm for the identification of near-native conformations generated by protein docking using experimental structures as well as protein models. The scoring function implemented in eRank(PPI) employs multiple features including interface probability estimates calculated by eFindSite(PPI) and a novel contact-based symmetry score. In comparative benchmarks using representative datasets of homo- and hetero-complexes, we show that eRank(PPI) consistently outperforms state-of-the-art algorithms improving the success rate by ~10Ā %. CONCLUSIONS: eRank(PPI) was designed to bridge the gap between the volume of sequence data, the evidence of binary interactions, and the atomic details of pharmacologically relevant protein complexes. Tolerating structure imperfections in computer-generated models opens up a possibility to conduct the exhaustive structure-based reconstruction of PPI networks across proteomes. The methods and datasets used in this study are available at www.brylinski.org/erankppi

    Development and Evaluation of a SYBR Green-Based Real-Time Multiplex RT-PCR Assay for Simultaneous Detection and Serotyping of Dengue and Chikungunya Viruses

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    10.1016/j.jmoldx.2015.06.008Journal of Molecular Diagnostics176722-728AfghanistanComplete

    Parental involvement in primary school education: its relationship with childrenā€™s academic performance and psychosocial competence through engaging children with school

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    The benefits of parental involvement in childrenā€™s education have been well established but increasing evidence suggests that overparenting may have adverse effects on children. The question of whether excessive parental involvement hinders childrenā€™s academic and psychosocial development warrants further investigations. This study examined the associations of parental educational involvement at home and in school with academic performance and psychological health of 507 Chinese Grade 3 schoolchildren in Hong Kong. Parents reported on their level of involvement in childrenā€™s schooling and their childrenā€™s psychosocial issues. Children were surveyed to determine their school engagement, and their Chinese language and mathematics attainment was assessed. We also explored the underlying mechanism by testing childrenā€™s engagement with school as a mediator of the relationships. Our results showed that home-based parental educational involvement was positively associated with childrenā€™s language competence and psychosocial wellbeing, and the associations were linked through engaging children with school. However, the benefits reached a plateau at higher level of parental involvement in childrenā€™s learning at home. School-based parental involvement had an indirect effect on childrenā€™s prosocial behavior through school engagement. These findings highlight the significance of optimal level of parental involvement in childrenā€™s education at home for childrenā€™s development
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