Evaluation of multiple protein docking structures using correctly predicted pairwise subunits

<p>Abstract</p> <p>Background</p> <p>Many functionally important proteins in a cell form complexes with multiple chains. Therefore, computational prediction of multiple protein complexes is an important task in bioinformatics. In the development of multiple protein docking methods, it is important to establish a metric for evaluating prediction results in a reasonable and practical fashion. However, since there are only few works done in developing methods for multiple protein docking, there is no study that investigates how accurate structural models of multiple protein complexes should be to allow scientists to gain biological insights.</p> <p>Methods</p> <p>We generated a series of predicted models (decoys) of various accuracies by our multiple protein docking pipeline, Multi-LZerD, for three multi-chain complexes with 3, 4, and 6 chains. We analyzed the decoys in terms of the number of correctly predicted pair conformations in the decoys.</p> <p>Results and conclusion</p> <p>We found that pairs of chains with the correct mutual orientation exist even in the decoys with a large overall root mean square deviation (RMSD) to the native. Therefore, in addition to a global structure similarity measure, such as the global RMSD, the quality of models for multiple chain complexes can be better evaluated by using the local measurement, the number of chain pairs with correct mutual orientation. We termed the fraction of correctly predicted pairs (RMSD at the interface of less than 4.0Å) as <it>fpair </it>and propose to use it for evaluation of the accuracy of multiple protein docking.</p

A cognitive framework for object recognition with application to autonomous vehicles

Autonomous vehicles or self-driving cars are capable of sensing the surrounding environment so they can navigate roads without human input. Decisions are constantly made on sensing, mapping and driving policy using machine learning techniques. Deep Learning – massive neural networks that utilize the power of parallel processing – has become a popular choice for addressing the complexities of real time decision making. This method of machine learning has been shown to outperform alternative solutions in multiple domains, and has an architecture that can be adapted to new problems with relative ease. To harness the power of Deep Learning, it is necessary to have large amounts of training data that are representative of all possible situations the system will face. To successfully implement situational awareness in driverless vehicles, it is not possible to exhaust all possible training examples. An alternative method is to apply cognitive approaches to perception, for situations the autonomous vehicles will face. Cognitive approaches to perception work by mimicking the process of human intelligence – thereby permitting a machine to react to situations it has not previously experienced. This paper proposes a novel cognitive approach for object recognition. The proposed cognitive object recognition algorithm, referred to as Recognition by Components, is inspired by the psychological studies pertaining to early childhood development. The algorithm works by breaking down images into a series of primitive forms such as square, triangle, circle or rectangle and memory based aggregation to identify objects. Experimental results suggest that Recognition by Component algorithm performs significantly better than algorithms that require large amounts of training data

Qualitätsmanagement in Theorie und Praxis

Qualitätsmanagement in Theorie und Praxis : e. Verbindung von Instrumenten d. empir. Sozialforschung u. d. Einsatz u. Nutzen für d. Praxis ; e. empir. Studie in e. süddt. Privatklinik. - München ; Mering : Hampp, 2001. - 357 S. - (Profession ; 29). - Zugl..: Augsburg, Univ., Diss., 200

100/300 Area Aquifer Tube Task: Annual Sampling for Fiscal Year 2006, Hanford Site, Washington

This letter report has been prepared to provide the U.S. Department of Energy, U.S. Environmental Protection Agency, Washington State Department of Ecology, and Hanford Site contractors with logistical information pertaining to the use of certain environmental monitoring sites. Although the distribution is not limited, It is not intended for general distribution beyond that audience