Difference between revisions of "Environment-Specific Protein Structural Alignment"

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(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...)
 
 
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|Student name=Leonardos Mageiros
 
|Student name=Leonardos Mageiros
 
|Project start date=2011/09/01
 
|Project start date=2011/09/01
|Project end date=2011/02/29
+
|Project end date=2011/03/01
 
|Supervisor=Gunnar Klau
 
|Supervisor=Gunnar Klau
 
|Second reader=Sanne Abeln
 
|Second reader=Sanne Abeln
 
|Company=CWI
 
|Company=CWI
 
|Thesis title=Environment-Specific Protein Structural Alignment
 
|Thesis title=Environment-Specific Protein Structural Alignment
|Finished=No
+
|Finished=Yes
 +
|Thesis=Thesis.pdf
 
|Poster=Image:Poster 27092011.pdf
 
|Poster=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.
 
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.

Latest revision as of 12:22, 27 June 2014


has title::Environment-Specific Protein Structural Alignment
status: finished
Master: project within::Internet and Web Technology
Student name: student name::Leonardos Mageiros
Dates
Start start date:=2011/09/01
End end date:=2011/03/01
Supervision
Supervisor: Gunnar Klau
Second reader: has second reader::Sanne Abeln
Company: has company::CWI
Thesis: has thesis::Media:Thesis.pdf
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.