Defining and Computing Optimum RMSD for Gapped and Weighted Multiple-Structure Alignment
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Multiple alignment of contact maps
IJCNN'09 Proceedings of the 2009 international joint conference on Neural Networks
Protein structure alignment using elastic shape analysis
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Recognition of finite structures with application to moving objects identification
ICAISC'10 Proceedings of the 10th international conference on Artificial intelligence and soft computing: Part I
Smolign: A Spatial Motifs-Based Protein Multiple Structural Alignment Method
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Formatt: correcting protein multiple structural alignments by sequence peeking
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
PRIB'12 Proceedings of the 7th IAPR international conference on Pattern Recognition in Bioinformatics
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Motivation: Existing comparisons of protein structures are not able to describe structural divergence and flexibility in the structures being compared because they focus on identifying a common invariant core and ignore parts of the structures outside this core. Understanding the structural divergence and flexibility is critical for studying the evolution of functions and specificities of proteins. Results: A new method of multiple protein structure alignment, POSA (Partial Order Structure Alignment), was developed using a partial order graph representation of multiple alignments. POSA has two unique features: (1) identifies and classifies regions that are conserved only in a subset of input structures and (2) allows internal rearrangements in protein structures. POSA outperforms other programs in the cases where structural flexibilities exist and provides new insights by visualizing the mosaic nature of multiple structural alignments. POSA is an ideal tool for studying the variation of protein structures within diverse structural families. Availability: POSA is freely available for academic users on a Web server at http://fatcat.burnham.org/POSA Contact:yye@burnham.org; adam@burnham.org