Yuzhen Ye1, Adam Godzik. 1. Program in Bioinformatics and Systems Biology, The Burnham Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA. yye@burnham.org
Abstract
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
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
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
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Authors: Debanu Das; Piotr Kozbial; Gye Won Han; Dennis Carlton; Lukasz Jaroszewski; Polat Abdubek; Tamara Astakhova; Herbert L Axelrod; Constantina Bakolitsa; Connie Chen; Hsiu Ju Chiu; Michelle Chiu; Thomas Clayton; Marc C Deller; Lian Duan; Kyle Ellrott; Marc André Elsliger; Dustin Ernst; Carol L Farr; Julie Feuerhelm; Anna Grzechnik; Joanna C Grant; Kevin K Jin; Hope A Johnson; Heath E Klock; Mark W Knuth; S Sri Krishna; Abhinav Kumar; David Marciano; Daniel McMullan; Mitchell D Miller; Andrew T Morse; Edward Nigoghossian; Amanda Nopakun; Linda Okach; Silvya Oommachen; Jessica Paulsen; Christina Puckett; Ron Reyes; Christopher L Rife; Natasha Sefcovic; Henry J Tien; Christine B Trame; Henry van den Bedem; Dana Weekes; Tiffany Wooten; Qingping Xu; Keith O Hodgson; John Wooley; Ashley M Deacon; Adam Godzik; Scott A Lesley; Ian A Wilson Journal: Acta Crystallogr Sect F Struct Biol Cryst Commun Date: 2009-10-27