By Roberto T. Alves, Myriam R. Delgado, Alex A. Freitas (auth.), Ana L. C. Bazzan, Mark Craven, Natália F. Martins (eds.)

This booklet constitutes the refereed court cases of the 3rd Brazilian Symposium on Bioinformatics, BSB 2008, held in Sao Paulo, Brazil, in August 2008 - co-located with IWGD 2008, the foreign Workshop on Genomic Databases.

The 14 revised complete papers and five prolonged abstracts have been rigorously reviewed and chosen from forty-one submissions. The papers handle a vast diversity of present subject matters in computational biology and bioinformatics that includes unique study in machine technological know-how, arithmetic and statistics in addition to in molecular biology, biochemistry, genetics, drugs, microbiology and different existence sciences.

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Extra info for Advances in Bioinformatics and Computational Biology: Third Brazilian Symposium on Bioinformatics, BSB 2008, Santo André, Brazil, August 28-30, 2008. Proceedings

Example text

These outputs, along with the true class (expected output) for each example, are used to generate the new training dataset. This dataset is then used to induce the meta-classifier, which is in charge of combining the Top-Down Hierarchical Ensembles of Classifiers 39 outputs from the base classifiers. In the test phase, the examples are given as inputs for each base classifier and the outputs of these classifiers are given as inputs of the meta-classifier, which performs the final classification. The main motivation for exploiting Top-Down algorithms based on ensemble methods is the advantage of using the combined power of several techniques instead of choosing just one of them to induce the classifier in each node of the class hierarchy.

This is important since the scoring function must be able to find, in the models, characteristics that are similar to the characteristics of native protein. An Evaluation of the Impact of Side Chain Positioning on the Accuracy 25 The first difficulty can be solved using a statistical scoring function. The second is the final step towards finding a near native structure and a number of techniques have been proposed. However, the search will only work if a good discrete model is available. The third difficulty is, therefore, the focus of this work.

Since there is a time limit, considering more rotamers or a more complex model may or may not produce better results. 5 Results To test the accuracy of discrete models we compiled a set of protein structures of increasing size. The proteins also differ in terms of secondary structure composition (Alpha Beta, Mainly Alpha and Mainly Beta proteins). Table 2 shows the set of chosen proteins and figure 3 shows the respective structures. We have chosen different types of proteins and different sizes to study the impact of these features in the precision of the discrete models.

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