Multiple flexible structure alignment using partial order graphs.
BACKGROUND
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.


BACKGROUND
POSA is freely available for academic users on a Web server at http://fatcat.burnham.org/POSA
Ye
Yuzhen
Y
Program in Bioinformatics and Systems Biology, The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA. yye@burnham.org
Godzik
Adam
A
D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D019143:Evolution, Molecular; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000032:analysis / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D013329:Structure-Activity Relationship
D011506:Proteins