Notice of RetractionSemi-local alignment algorithms for three dimensional protein structures comparison

Notice of Retraction

After careful and considered review of the content of this paper by a duly constituted expert committee, this paper has been found to be in violation of IEEE´s Publication Principles.

We hereby retract the content of this paper. Reasonable effort should be made to remove all past references to this paper.

The presenting author of this paper has the option to appeal this decision by contacting TPII@ieee.org.

Protein structures are essential for correct biological functions because similar structures between proteins allow molecular recognition. Identifying similar structures between proteins provide the opportunity to recognize homology that is undetectable by sequence comparison. Thus comparison and alignment of protein structures represents a powerful means of discovering functions, yielding direct insight into the molecular mechanisms. Currently, there are several techniques available in attempting to find the optimal alignment of shared structural motifs between two proteins. In this paper, we propose algorithms and develop tools for local alignment between two protein structures by the technique of semi-local alignment between the carbon atoms of two proteins. These initialized alignment algorithms are later refined by our previously proposed methods by stepwise finding better alignments of the protein pairings using minimum bipartite matching method on geometric distance space and several other adjustment strategies in estimating good isometric transformations based on trigonometric series approximation. We show the effectiveness of the proposed semi-local alignment algorithm by a set of experiments, which improve several previous results. Furthermore, some of our preliminary result is accessible through the web interface.