R. Kolodny and N. Linial (2004), Approximate Protein Structural Alignment in Polynomial Time, Proc. Natl. Acad. Sci. USA, 101 (33) , 12201-12206.


Protein structural alignment is a fundamental problem in computational structural biology. Here, we study it as a family of optimization problem and provide a polynomial time algorithm to solve them. We also show an NP-hardness proof of an alternative approach to this problem using internal distance matrices. Lastly, we visualize the scoring function for several pairs of structures.


  AUTHOR =       "Kolodny, R. and Linial, N.",
  TITLE =        "Approximate Protein Structural Alignment in Polynomial Time",
  JOURNAL =      "Proc. Natl. Acad. Sci. (USA)",
  YEAR =         "2004",
  volume =       "101",
  pages =        "12201 -- 12206",