A Parameterized Algorithm for Protein Structure Alignment

  title={A Parameterized Algorithm for Protein Structure Alignment},
  author={Jinbo Xu and Feng Jiao and Bonnie Berger},
  journal={Journal of computational biology : a journal of computational molecular cell biology},
  volume={14 5},
This paper proposes a parameterized polynomial time approximation scheme (PTAS) for aligning two protein structures, in the case where one protein structure is represented by a contact map graph and the other by a contact map graph or a distance matrix. If the sequential order of alignment is not required, the time complexity is polynomial in the protein size and exponential with respect to two parameters D(u)/D(l) and D(c)/D(l), which usually can be treated as constants. In particular, D(u) is… CONTINUE READING
Highly Cited
This paper has 69 citations. REVIEW CITATIONS


Publications citing this paper.
Showing 1-10 of 33 extracted citations

69 Citations

Citations per Year
Semantic Scholar estimates that this publication has 69 citations based on the available data.

See our FAQ for additional information.


Publications referenced by this paper.
Showing 1-10 of 26 references

Rapid side-chain packing via tree decomposition

  • J. Xu
  • In RECOMB 2005, volume 3500 of Lecture Notes in…
  • 2005
2 Excerpts

Similar Papers

Loading similar papers…