By Bastiaan A. van den Berg, Jurgen F. Nijkamp, Marcel J. T. Reinders, Liang Wu (auth.), Tjeerd M. H. Dijkstra, Evgeni Tsivtsivadze, Elena Marchiori, Tom Heskes (eds.)
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Additional resources for Pattern Recognition in Bioinformatics: 5th IAPR International Conference, PRIB 2010, Nijmegen, The Netherlands, September 22-24, 2010. Proceedings
However, it may be useful to study the regularities in RNA free energy measurements in the laboratory to guide choices in how covariance models are constructed. From the laboratory, we know that the identities of the nucleotides at the interface between the stem and the loop of a hairpin structure greatly affect thermodynamic stability of the hairpin structure. We also know that the length of the loop is a factor in stability. The mechanisms to capture these regularities are weak and nonexistent, respectively, in current covariance modeling practice.
Biopolymers 85, 456–470 (2007) 3. : DNA recognition code of transcription factors. Protein Engineering 8, 319–328 (1995) 4. : Is there a code for protein-DNA recognition? Probab(ilistical)ly. Bioessays 24, 466–475 (2002) 5. : Protein-DNA interactions: amino acid conservation and the eﬀects of mutations on binding speciﬁcity. Journal of Molecular Biology 320, 991–1009 (2002) 6. : An overview of the structures of protein-DNA complexes. Genome Biology 1, REVIEWS001 (2000) 7. : Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics.
The heatmap shows that the molecules in the two extremes of the multilabel distribution form groups of high similarity whereas the molecules in the middle are much more dissimilar both to each other and to the extreme groups. The result seems to indicate that the majority of molecules in the dataset are either very speciﬁc or very general in the targets they are active against. 2 produce a similar heatmap indicating that the phenomenon is not kernel-speciﬁc. 6 0 10 20 30 40 50 Number of active cell lines Fig.
Pattern Recognition in Bioinformatics: 5th IAPR International Conference, PRIB 2010, Nijmegen, The Netherlands, September 22-24, 2010. Proceedings by Bastiaan A. van den Berg, Jurgen F. Nijkamp, Marcel J. T. Reinders, Liang Wu (auth.), Tjeerd M. H. Dijkstra, Evgeni Tsivtsivadze, Elena Marchiori, Tom Heskes (eds.)