The GABI Primary Database, GabiPD (http:// www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different ‘omics’ fronts are incorporated (i.e. genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for textbased retrieval of all data types in GabiPD (e.g. clones, genes, mutant lines). All data types point to a central Gene GreenCard, where gene information is integrated from genome projects or NCBI UniGene sets. The centralized Gene GreenCard allows visualizing ESTs aligned to annotated transcripts as well as displaying identified protein domains and gene structure. Moreover, GabiPD makes available interactive genetic maps from potato and barley, and protein 2DE gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic-profiling data can be visualized through MapManWeb. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of the data.

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Protein phosphorylation is a common post-translational protein modification used in almost all cellular processes. When a phosphate group is added to an amino acid side chain, it may alter the protein conformation and protein-protein interactions due to its size and its negative charge. It may also change the protein function, activity and even localization within the cell. Experimental detection of phosphorylation is still extremely labor demanding and very expensive, even when deploying protein mass spectrometry. For this very reason many bioinformatics scientific groups focus on the prediction of protein phosphorylation sites. Recent analyses of phosphorylation sites studied mainly non-phosphorylated phosphorylation sites and the distribution and representation of amino acids sequentially neighboring them. Since sequentially more distant, but structurally close amino acids can contribute to the recognition of protein substrate by protein kinase, structural environment of phosphorylation sites was studied in this thesis. Furthermore, 3D structures of phosphorylation sites were comprehensively studied for the first time in a phosphorylated state and the results were compared with the results obtained from the analysis of non- phosphorylated sites. Phosphorylation sites were found mostly within...