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.
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.
Authors: Esther León; Adelinda Yee; Angel R Ortíz; Jorge Santoro; Manuel Rico; M Angeles Jiménez Journal: Protein Sci Date: 2007-08-31 Impact factor: 6.725
Authors: M S Madhusudhan; Benjamin M Webb; Marc A Marti-Renom; Narayanan Eswar; Andrej Sali Journal: Protein Eng Des Sel Date: 2009-07-08 Impact factor: 1.650
Authors: Ben Webb; Andrej Sali; Narayanan Eswar; Marc A Marti-Renom; M S Madhusudhan; David Eramian; Min-Yi Shen; Ursula Pieper Journal: Curr Protoc Bioinformatics Date: 2006-10