Characterization of phosphorylation sites using 3D structural information

Protein Phosphorylation is one of the most important and most studied modifications that a protein can undergo after its translation (post translational modifications). This is also a field in which bioinformatics efforts are most helpful understanding this fundamental process and, in particular, to predict protein phosphorylation. Since this problem has began an important bioinformatics research topic, about 20 years ago, for a number of reasons (lack of data, misleading assumption, etc) it has, almost always, been treated mostly with sequence-based methods. Although the local amino acid sequence may contain a significant part of the information contents related to phosphorylation, the local spatial environment may contribute significantly to the specificity of molecular event. Based on this consideration, the aim of this thesis is to explore ways in which three dimensional information can help to better understand and characterize protein phosphorylation mechanisms. This thesis is organized as follows. First, in Chapter 1 a simple biological basis is provided to understand the argument treated. Chapter 2, after a review of current bioinformatics literature, presents the aims of this thesis in details, and the methods used to solve them. In Chapter 3 the software developed and implemented is analyzed and described. Then in Chapter 4 the results obtained with the software developed are presented with a detailed analysis. In the end in Chapter 5 a short summary of the work done and a discussion about future developments are given