Environment-Specific Protein Structural Alignment
From Master Projects
Revision as of 15:20, 15 November 2011 by Lms450 (talk | contribs) (New page: {{Masterproject |Master name=Internet and Web Technology |Student name=Leonardos Mageiros |Project start date=2011/09/01 |Project end date=2011/02/29 |Supervisor=Gunnar Klau |Second reader...)
| has title::Environment-Specific Protein Structural Alignment | |
|---|---|
status: ongoing
| |
| Master: | project within::Internet and Web Technology |
| Student name: | student name::Leonardos Mageiros |
| Dates | |
| Start | start date:=2011/09/01 |
| End | end date:=2011/02/29 |
| Supervision | |
| Supervisor: | Gunnar Klau |
| Second reader: | has second reader::Sanne Abeln |
| Company: | has company::CWI |
| Poster: | has poster::Media:Image:Poster 27092011.pdf |
Signature supervisor
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Abstract
We use a general mathematical model for optimal pairwise protein structure alignment. The model is based on aligning inter-residue distance matrices and supports structural and sequence scores as well as affine gap costs. PAUL, an algorithm that is based on this model is currently competitive with state-of-the art structural alignment methods in terms of alignment accuracy. The purpose of this thesis is to further improve the biological relevance of PAUL by integrating additional features such as environment-specific amino acid substitution tables and gap cost penalties.
