Characterization, classification and alignment of protein-protein interfaces [Elektronische Ressource] / Zhu, Hongbo

Characterization, Classi cation and Alignmentof Protein-Protein InterfacesZhu, HongboA DissertationSubmitted to the Faculty ofNatural Sciences and Technology IMathematics and Computer ScienceSaarland UniversityIn Partial Ful llment of theRequirements for the Degree ofDoktor der Naturwissenschaften (Dr. rer. nat.)Saarbruc ken2010Date of Colloquium: 24-06-2010Dean of the Faculty: Prof. Dr. Holger HermannsChairman: Prof. Dr. Hans-Peter LenhofDoctorate Committee Members: Prof. Dr. Dr. Thomas LengauerProf. Dr. Peter LacknerTo my parents.viiAbstractProtein structural models provide essential information for the research on protein-protein interactions. In this dissertation, we describe two projects on the analysis ofprotein interactions using structural information. The focus of the rst is to charac-terize and classify di erent types of interactions. We discriminate between biologicalobligate and biological non-obligate interactions, and crystal packing contacts. Tothis end, we de ned six interface properties and used them to compare the threetypes of interactions in a hand-curated dataset. Based on the analysis, a classi- er, named NOXclass, was constructed using a support vector machine algorithmin order to generate predictions of interaction types. NOXclass was tested on anon-redundant dataset of 243 protein-protein interactions and reaches an accuracyof 91.8%.