We address the problem of aligning the 3D structures of two proteins. Our pairwise comparisons are based on a new optimization model that is succinctly expressed in terms of linear transformations and highlights the problem’s intrinsic geometry. The optimization problem is approximately solved with a new polynomial time algorithm. The worst case analysis of the algorithm shows that the solution is bounded by a constant depending only on the data of the problem.
Shibberu, Yosi; Holder, Allen; and Lutz, Kyla, "Fast Protein Structure Alignment" (2010). Mathematical Sciences Technical Reports (MSTR). 22.