Environment-Specific Protein Structural Alignment
|has title::Environment-Specific Protein Structural Alignment|
|Master:||project within::Internet and Web Technology|
|Student name:||student name::Leonardos Mageiros|
|Second reader:||has second reader::Sanne Abeln|
|Poster:||has poster::Media:Image:Poster 27092011.pdf|
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.