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
The use of a conformational alphabet for fast alignment of protein structures
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
Research Article: Bacterial protein structures reveal phylum dependent divergence
Computational Biology and Chemistry
Smolign: A Spatial Motifs-Based Protein Multiple Structural Alignment Method
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Defining and computing optimum RMSD for gapped multiple structure alignment
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
PRIB'12 Proceedings of the 7th IAPR international conference on Pattern Recognition in Bioinformatics
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Motivation: Multiple structure alignments are becoming important tools in many aspects of structural bioinformatics. The current explosion in the number of available protein structures demands multiple structural alignment algorithms with an adequate balance of accuracy and speed, for large scale applications in structural genomics, protein structure prediction and protein classification. Results: A new multiple structural alignment program, MAMMOTH-mult, is described. It is demonstrated that the alignments obtained with the new method are an improvement over previous manual or automatic alignments available in several widely used databases at all structural levels. Detailed analysis of the structural alignments for a few representative cases indicates that MAMMOTH-mult delivers biologically meaningful trees and conservation at the sequence and structural levels of functional motifs in the alignments. An important improvement over previous methods is the reduction in computational cost. Typical alignments take only a median time of 5 CPU seconds in a single R12000 processor. MAMMOTH-mult is particularly useful for large scale applications. Availability: http://ub.cbm.uam.es/mammoth/mult Contact: aro@cbm.uam.es