Title: "Flexible Structure Alignment"
Speaker: Yuzhen Ye, School of Informatics, Indiana University, Bloomington, IN
Place: Mechanical Engineering (ME) 161; February 12, 2008, Tuesday, 4:30pm


Protein structure comparison is a classic bioinformatics problem that has many applications including structure-based similarity searching and functional annotation. Protein structures are flexible and undergo structural rearrangements as part of their function. Only recently, several general-purpose pairwise and multiple structure alignment programs that incorporate protein structural flexibility have been developed. In this talk, I will introduce the methodology of a pairwise (FATCAT) and a multiple (POSA) flexible structure comparison approach that we have developed. FATCAT formulates the problem of flexible structure alignment as a chaining process of aligned fragment pairs (AFP) allowing a limited number of twists (conformational changes). POSA adopts a partial order graph representation of multiple alignments so that it can capture partially conserved regions. I will also briefly introduce a recent development, TOP2FATCAT, which is a faster flexible structure comparison approach using constraints from TOPStrings models.

Associated Reading:
Yuzhen Ye and Adam Godzik. 2005. Multiple flexible structure alignment using partial order graphs. Bioinformatics, 21(10):2362-2369

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