RECOMB '01 Proceedings of the fifth annual international conference on Computational biology
An Efficient Lagrangian Relaxation for the Contact Map Overlap Problem
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
Structural Bioinformatics: An Algorithmic Approach
Structural Bioinformatics: An Algorithmic Approach
Bioinformatics
Algorithms for optimal protein structure alignment
Bioinformatics
Evaluating Protein Similarity from Coarse Structures
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fast Hinge Detection Algorithms for Flexible Protein Structures
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fast protein structure alignment
ISBRA'10 Proceedings of the 6th international conference on Bioinformatics Research and Applications
Using dominances for solving the protein family identification problem
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
3D partial surface matching using differential geometry and statistical approaches
IScIDE'12 Proceedings of the third Sino-foreign-interchange conference on Intelligent Science and Intelligent Data Engineering
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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.