Matt: local flexibility aids protein multiple structure alignment

PLoS Computational Biology
Matthew MenkeLenore J Cowen

Abstract

Even when there is agreement on what measure a protein multiple structure alignment should be optimizing, finding the optimal alignment is computationally prohibitive. One approach used by many previous methods is aligned fragment pair chaining, where short structural fragments from all the proteins are aligned against each other optimally, and the final alignment chains these together in geometrically consistent ways. Ye and Godzik have recently suggested that adding geometric flexibility may help better model protein structures in a variety of contexts. We introduce the program Matt (Multiple Alignment with Translations and Twists), an aligned fragment pair chaining algorithm that, in intermediate steps, allows local flexibility between fragments: small translations and rotations are temporarily allowed to bring sets of aligned fragments closer, even if they are physically impossible under rigid body transformations. After a dynamic programming assembly guided by these "bent" alignments, geometric consistency is restored in the final step before the alignment is output. Matt is tested against other recent multiple protein structure alignment programs on the popular Homstrad and SABmark benchmark datasets. Matt's global perfor...Continue Reading

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Methods Mentioned

BETA
protein folding

Software Mentioned

FlexProt
DeepView )
MultiProt
Swiss PDB Viewer (
Mattâthe
SolidAngle
LocalOpt
Windows
Linux
Rasmol script

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