By Bernard M. E. Moret (auth.), Aaron Darling, Jens Stoye (eds.)
This publication constitutes the refereed court cases of the thirteenth overseas Workshop on Algorithms in Bioinformatics, WABI 2013, held in Sophia Antipolis, France, in September 2013. WABI 2013 is one among seven workshops which, besides the eu Symposium on Algorithms (ESA), represent the ALGO annual assembly and highlights examine in algorithmic paintings for bioinformatics, computational biology and structures biology. The target is to provide fresh learn effects, together with major work-in-progress, and to spot and discover instructions of destiny study. The 27 complete papers awarded have been conscientiously reviewed and chosen from sixty one submissions. The papers hide all points of algorithms in bioinformatics, computational biology and platforms biology.
Read Online or Download Algorithms in Bioinformatics: 13th International Workshop, WABI 2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings PDF
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Additional resources for Algorithms in Bioinformatics: 13th International Workshop, WABI 2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings
The unclustered ROTRANs are treated as noise. Similar approximate clustering algorithms have been used  and studied . To complete the clustering algorithm, we need a distance function between ROTRANs. The Riemannian distance is a widely used distance metric measuring the length of the shortest geodesic curve between two rotation matrices . Since the transition vector can be calculated by the rotation matrix and the weight centers of the aligned residues, we use Riemannian distances between rotation matrices to avoid using redundant information when clustering ROTRANs.
2 Protein Structure Alignment Scoring Function TM-score , based on LG-score , is one of the most successful protein structure alignment scoring functions. However, one limitation of TM-score and LG-score is that they use only protein structure similarity while they ignore other protein similarities, such as the sequence similarity. It has been observed that many protein structure alignments, based only on protein structure similarity, are highly sensitive to conformational changes .
Nucleic Acids Res. 28, 235–242 (2000) 2. : Protein structure comparison using representation by line segment sequences. In: Pac. Symp. , pp. 25–40 (1996) 3. : SARFing the PDB. Protein Eng. 9(9), 727–732 (1996) 4. : Structural alignment of large-size proteins via lagrangian relaxation. In: RECOMB 2002: Proceedings of the Sixth Annual International Conference on Computational Biology, pp. 100–108. ACM, New York (2002) 5. : Proust: a comparison method of threedimensional structure of proteins using indexing techniques.