title: Determining protein similarity by comparing hydrophobic core structure.
abstract: Formal assessment of structural similarity is - next to protein structure prediction - arguably the most important unsolved problem in proteomics. In this paper we propose a similarity criterion based on commonalities between the proteins' hydrophobic cores. The hydrophobic core emerges as a result of conformational changes through which each residue reaches its intended position in the protein body. A quantitative criterion based on this phenomenon has been proposed in the framework of the CASP challenge. The structure of the hydrophobic core - including the placement and scope of any deviations from the idealized model - may indirectly point to areas of importance from the point of view of the protein's biological function. Our analysis focuses on an arbitrarily selected target from the CASP11 challenge. The proposed measure, while compliant with CASP criteria (70-80% correlation), involves certain adjustments which acknowledge the presence of factors other than simple spatial arrangement of solids.
authors.affiliation: AGH - Academic Computer Center - Cyfronet, Nawojki 11, Kraków 30-950, Poland.
authors.forename: M
authors.initials: M
authors.lastname: Gadzała
authors.affiliation: Faculty of Physics, Astronomy, Applied Computer Science - Jagiellonian University, Łojasiewicza 11, Kraków 30-348, Poland.
authors.forename: B
authors.initials: B
authors.lastname: Kalinowska
authors.affiliation: Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College, Łazarza 16, Krakow 31-530, Poland.
authors.forename: M
authors.initials: M
authors.lastname: Banach
authors.affiliation: Chair of Medical Biochemistry, Jagiellonian University - Medical College, Kopernika 7, Kraków 31-034, Poland.
authors.forename: L
authors.initials: L
authors.lastname: Konieczny
authors.affiliation: Department of Bioinformatics and Telemedicine, Jagiellonian University - Medical College, Łazarza 16, Krakow 31-530, Poland.
authors.forename: I
authors.initials: I
authors.lastname: Roterman
keywords: Bioinformatics; Biological sciences