By Mitra Basu, Yi Pan, Jianxin Wang
This ebook constitutes the refereed lawsuits of the tenth foreign Symposium on Bioinformatics learn and functions, ISBRA 2014, held in Zhangjiajie, China, in June 2014. The 33 revised complete papers and 31 one-page abstracts incorporated during this quantity have been conscientiously reviewed and chosen from 119 submissions. The papers disguise a variety of themes in bioinformatics and computational biology and their functions together with the improvement of experimental or advertisement systems.
Read Online or Download Bioinformatics Research and Applications: 10th International Symposium, ISBRA 2014, Zhangjiajie, China, June 28-30, 2014. Proceedings PDF
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Additional resources for Bioinformatics Research and Applications: 10th International Symposium, ISBRA 2014, Zhangjiajie, China, June 28-30, 2014. Proceedings
Given two proteins P and Q of length m and n respectively. , (pik , qjk )}, where 1 ≤ i1 < i2 < ... < ik ≤ m and 1 ≤ j1 = j2 = ... , n}, that optimizes some similarity measure for the above correspondence. Deﬁnition 3. A residue pi of a protein P is known as a k-neighbor of another residue pj if |i − j| = k, where 1 ≤ i, j ≤ |P |. 2 Similarity Measures To measure the extent of structural similarity of two proteins, the root mean square deviation (RM SD) is widely used [26, 29]. Two diﬀerent RM SD measures have been proposed in the literature: (1) coordinate root mean square deviation (cRM SD) and (2) distance root mean square deviation (dRM SD).
The latter two steps are repeated until there is no improvement in the alignment. These methods are able to provide sequence and topology independent similarities. The reason for this is that the primary equivalence set (residues-pairs for equal length proteins and SSE-pairs for unequal length proteins) depends on the intrinsic geometry of α-the carbon atoms within the tertiary structure that is revealed by eigendecomposition. We report the TM-score and cRM SD as measures of the structural similarity.
A similar observation has been made by other researchers [12, 26, 31, 32]. To circumvent this problem, Zhang and Skolnick  introduced a sequence independent structural alignment measure (TM-score) that is a variation of a measure originally deﬁned by Levitt and Gerstein . A critical assessment of this TM-score has been given by Xu and Zhang . Deﬁnition 5. 8) is a normalization factor. Ch. Panigrahi and A. Mukhopadhyay When the value of d0 in equation (3) is set to 5Ao , the resulting TM-score is known as a raw TM-score (rTM-score).