Download e-book for iPad: Advances in Bioinformatics and Computational Biology: Third by Roberto T. Alves, Myriam R. Delgado, Alex A. Freitas

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

ISBN-10: 3540855564

ISBN-13: 9783540855569

ISBN-10: 3540855572

ISBN-13: 9783540855576

This e-book 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 conscientiously reviewed and chosen from forty-one submissions. The papers tackle a huge diversity of present themes in computational biology and bioinformatics that includes unique examine in machine technology, arithmetic and facts in addition to in molecular biology, biochemistry, genetics, medication, microbiology and different existence sciences.

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Read or Download Advances in Bioinformatics and Computational Biology: Third Brazilian Symposium on Bioinformatics, BSB 2008, Santo André, Brazil, August 28-30, 2008. Proceedings PDF

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

Example text

In a six state model that space will be even greater. We can probably achieve the same result from a four states model after a refinement process and we would benefit greatly from the smaller size of the search space during the search process. From figures 4 and 5 we can see the impact of the size of the rotamer library in the search. The performance of the models usually increases with the size of the rotamer library. However it is possible to verify that, for the bigger or more compact proteins, the performance sometimes decreases.

The best n states are chosen and the same steps are iterated until the final configurations are reached. Although the beam search method obtained good results in the backbone only problem [5], for the problem presented here the results were much worse. In fact, when the protein size was greater than 80 amino acids, a solution with an RMSD near five angstrom was difficult to obtain with this method. The beam search approach is a non exact method. An explanation for this, already presented by Park and Levitt [5] for the backbone fitting problem, is that the neglected search states, although with worse RMSD values at the time they were removed from search, may in reality provide better fits in the long run.

Without an exact measure, the number of wrong conformations searched will be much greater and the increased computational cost of the enlarged library will further decrease the performance. The type of model used and the threshold limit will have to be chosen according to the type of proteins (specially their secondary structure and size) and the search algorithm. For a search algorithm, with no specific information, a four states model, specially a generic one like the C model, with a side chain threshold An Evaluation of the Impact of Side Chain Positioning on the Accuracy 33 of 1% will probably have best results because of the increase in the size of the searched space.

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Advances in Bioinformatics and Computational Biology: Third Brazilian Symposium on Bioinformatics, BSB 2008, Santo André, Brazil, August 28-30, 2008. Proceedings by Roberto T. Alves, Myriam R. Delgado, Alex A. Freitas (auth.), Ana L. C. Bazzan, Mark Craven, Natália F. Martins (eds.)


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