Finding longest common segments in protein structures in nearly linear time

Yen Kaow Ng, Hirotaka Ono, Ling Ge, Shuai Cheng Li

研究成果: 著書/レポートタイプへの貢献会議での発言

抜粋

The Local/Global Alignment (Zemla, 2003), or LGA, is a popular method for the comparison of protein structures. One of the two components of LGA requires us to compute the longest common contiguous segments between two protein structures. That is, given two structures A = (a 1, ..., a n ) and B = (b 1, ..., b n ) where a k , b k ∈ ℝ 3, we are to find, among all the segments f = (a i ,...,a j ) and g = (b i ,...,b j ) that fulfill a certain criterion regarding their similarity, those of the maximum length. We consider the following criteria: (1) the root mean square deviation (RMSD) between f and g is to be within a given t ∈ ℝ; (2) f and g can be superposed such that for each k, i ≤ k ≤ j, ||a k - b k || ≤ t for a given t ∈ . We give an algorithm of time complexity when the first requirement applies, where is the maximum length of the segments fulfilling the criterion. We show an FPTAS which, for any ε∈ ℝ, finds a segment of length at least l, but of RMSD up to (1 + ε)t, in O(nlogn + n/ε) time. We propose an FPTAS which for any given ε∈ ℝ, finds all the segments f and g of the maximum length which can be superposed such that for each k, i ≤ k ≤ j, ||a k - b k || ≤ (1 + ε) t, thus fulfilling the second requirement approximately. The algorithm has a time complexity of O(nlog 2 n/ε 5) when consecutive points in A are separated by the same distance (which is the case with protein structures).

元の言語英語
ホスト出版物のタイトルCombinatorial Pattern Matching - 23rd Annual Symposium, CPM 2012, Proceedings
ページ334-348
ページ数15
DOI
出版物ステータス出版済み - 7 4 2012
イベント23rd Annual Symposium on Combinatorial Pattern Matching, CPM 2012 - Helsinki, フィンランド
継続期間: 7 3 20127 5 2012

出版物シリーズ

名前Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
7354 LNCS
ISSN(印刷物)0302-9743
ISSN(電子版)1611-3349

その他

その他23rd Annual Symposium on Combinatorial Pattern Matching, CPM 2012
フィンランド
Helsinki
期間7/3/127/5/12

    フィンガープリント

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)

これを引用

Ng, Y. K., Ono, H., Ge, L., & Li, S. C. (2012). Finding longest common segments in protein structures in nearly linear time. : Combinatorial Pattern Matching - 23rd Annual Symposium, CPM 2012, Proceedings (pp. 334-348). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); 巻数 7354 LNCS). https://doi.org/10.1007/978-3-642-31265-6_27