| The problem of inferring the function of a protein in the context of the complex network of interactions is one of the most crucial challenges faced by Computational Biology today. Knowing the binding partners of proteins is an essential step to untangle the web of functional relationships that control cellular processes, and the identification and the characterization of a protein binding site represent an important step to achieve this goal. Some of the most widely used techniques that have been developed by the bioinformatics community over the years are discussed here, together with their limitations and applicability range.;This thesis introduces a framework to perform binding site identification on protein structures by means of an energy-based approach based on the concept of Molecular Interaction Fields (MIFs). The approach has been validated on a large set of bound and unbound protein structures, and a specific application of binding site identification in the context of reverse virtual screening is discussed. The advantage of using chemically specific probes to compute the MIFs is illustrated by applying the binding site identification procedure to phosphorylated ligands. Furthermore, an improved version of the energy-based binding site identification approach that incorporates evolutionary information is presented, emphasizing its advantage in situations where the energy-based signal is weak.;As an attempt to move beyond the problem of binding site identification, a methodology that can be applied to infer the bound conformation of a protein starting from an unbound form is introduced.;Taken together, the results presented in this work indicate that the energy-based approach with multiple probes MIFs provides a versatile framework to carry out binding site identification and hint to the possibility of identifying the bound form of structures that undergo large conformational changes. Furthermore, the problem of predicting the type of ligand that a binding site can accommodate lies among the future challenges that could benefit from the methodology described here. |
