Name
Abstract | ||
|---|---|---|
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=(a1, …, an) and B=(b1, …, bn) where ak, bk∈ℝ3, we are to find, among all the segments f=(ai,…,aj) and g=(bi,…,bj) 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, ||ak−bk||≤t for a given t∈ℝ. We give an algorithm of $O(n\log n+n\mbox{\it \textbf{l}})$ time complexity when the first requirement applies, where $\mbox{\it \textbf{l}}$ 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, ||ak−bk||≤(1+ε) t, thus fulfilling the second requirement approximately. The algorithm has a time complexity of O(nlog2n/ε5) when consecutive points in A are separated by the same distance (which is the case with protein structures). |
Year | DOI | Venue |
|---|---|---|
2012 | 10.1007/978-3-642-31265-6_27 | CPM |
Keywords | Field | DocType |
global alignment,following criterion,maximum length,consecutive point,longest common contiguous segment,protein structure,linear time,certain criterion,popular method,log n,longest common segment,time complexity | Discrete mathematics,Protein structure prediction,Binary logarithm,Combinatorics,Pairwise sequence alignment,Root-mean-square deviation,Time complexity,Mathematics,Protein structure | Conference |
Citations | PageRank | References |
0 | 0.34 | 7 |
Authors | ||
4 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Yen Kaow Ng | 1 | 73 | 9.46 |
| Hirotaka Ono | 2 | 400 | 56.98 |
| Ling Ge | 3 | 0 | 0.34 |
| Shuai Cheng Li | 4 | 184 | 30.25 |