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Various molecular docking software packages are available for modeling interactions between small molecules and proteins.However,there have been few reports of modeling the interactions between metal ions and metalloproteins.In this study,the AutoDock package was employed to example docking into a di-iron binding protein,bacterioferritin.Each binding site of this protein was tested for docking with iron ions.Blind docking experiments showed that all docking conformations converged into two clusters,one for internal iron binding in sites within the metalloprotein and the other for external iron binding on the protein surface.Local docking experiments showed that there were significant differences between two internal iron binding sites.Docking at one site gave a reasonable root-mean-square deviation(RMSD) distribution with relatively low binding energy.Analysis of the binding mode quality for this site revealed that more than half of the docking conformations were categorized as having good binding geometry,while no good conformations were found for the other site.Further investigations indicated that coordinating water molecules contributed to the stability of binding geometries.This study provides an empirical approach towards the study of molecular docking in metalloproteins. 相似文献
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From the viewpoint of service level agreements,data transmission accuracy is one of the critical performances for assessing Internet by service providers and enterprise customers.The stochastic computer network(SCN),in which each edge has several capacities and the accuracy rate,has multiple terminals.This paper is aimed mainly to evaluate the system reliability for an SCN,where system reliability is the probability that the demand can be fulfilled under the total accuracy rate.A minimal capacity vector allows the system to transmit demand to each terminal under the total accuracy rate.This study proposes an efficient algorithm to find all minimal capacity vectors by minimal paths.The system reliability can then be computed in terms of all minimal capacity vectors by the recursive sum of disjoint products(RSDP) algorithm. 相似文献
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《小型微型计算机系统》2011,32(9)
一、征稿范围:《小型微型计算机系统》杂志刊登文章的内容涵盖计算技术的各个领域(计算数学除外).包括计算机科学理论、体系结构、计算机软件、数据库、网络与通讯、人工智能、信息安全、多媒体、计算机图形与图像、算法理论研究等各方面的学术论文. 相似文献