Environment-Specific Protein Structural Alignment

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has title::Environment-Specific Protein Structural Alignment
status: ongoing
Master: project within::Internet and Web Technology
Student name: student name::Leonardos Mageiros
Start start date:=2011/09/01
End end date:=2011/02/29
Supervisor: Gunnar Klau
Second reader: has second reader::Sanne Abeln
Company: has company::CWI
Poster: has poster::Media:Image:Poster 27092011.pdf

Signature supervisor



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.