Issue No. 04 - July/August (2011 vol. 8)
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.24
Allen Holder , Rose-Hulman Institute of Technology, Terre Haute
Yosi Shibberu , Rose-Hulman Institute of Technology, Terre Haute
A new intrinsic geometry based on a spectral analysis is used to motivate methods for aligning protein folds. The geometry is induced by the fact that a distance matrix can be scaled so that its eigenvalues are positive. We provide a mathematically rigorous development of the intrinsic geometry underlying our spectral approach and use it to motivate two alignment algorithms. The first uses eigenvalues alone and dynamic programming to quickly compute a fold alignment. Family identification results are reported for the Skolnick40 and Proteus300 data sets. The second algorithm extends our spectral method by iterating between our intrinsic geometry and the 3D geometry of a fold to make high-quality alignments. Results and comparisons are reported for several difficult fold alignments. The second algorithm's ability to correctly identify fold families in the Skolnick40 and Proteus300 data sets is also established.
Protein structure alignment, structural bioinformatics, contact maps, spectral methods.
Allen Holder, Yosi Shibberu, "A Spectral Approach to Protein Structure Alignment", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. , pp. 867-875, July/August 2011, doi:10.1109/TCBB.2011.24