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