By Roberto T. Alves, Myriam R. Delgado, Alex A. Freitas (auth.), Ana L. C. Bazzan, Mark Craven, Natália F. Martins (eds.)
This publication 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 overseas 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 large variety of present subject matters in computational biology and bioinformatics that includes unique study in laptop technological know-how, arithmetic and information in addition to in molecular biology, biochemistry, genetics, drugs, microbiology and different existence sciences.
Read Online 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 info for Advances in Bioinformatics and Computational Biology: Third Brazilian Symposium on Bioinformatics, BSB 2008, Santo André, Brazil, August 28-30, 2008. Proceedings
35–46, 2008. P. Costa et al. consequent generation of biological data in large scale, data analysis has become a central issue for the investigation of proteins whose functions are unknown. An approach that can be used in the prediction of a protein function involves searching against secondary databases, also known as signature databases. These databases contain results of analysis performed in primary databases, which contain linear sequences of amino acids, and can be used to verify the presence of particular patterns in the query proteins.
We extend the work of Park and Levitt by taking into account the positioning of the side chain in the evaluation of the accuracy. We show that the problem becomes much harder and more dependent on the type of protein being modeled. In fact, the structure ﬁtting method used in their work is no longer adequate to this extended version of the problem. We propose a new method to test the model accuracy. The presented results show that, for some proteins, the discrete models with side chains cannot achieve the accuracy of the backbone only discrete models.
The algorithm does a simple beam search using the RMSD distance as the scoring function. In a beam search, n states are saved at any given time. Considering that there are m choices in an m state discrete model, the algorithm starts by testing the ﬁrst m choices. The algorithm then chooses the best n states and tests all the choices for each of those states (n × m tests). 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 , for the problem presented here the results were much worse.