The work in this thesis is divided into two aims. The first aim is to provide a detailed analysis of water molecules at protein-protein interfaces as well as quantifying their contributions with respect to different residue types. To achieve this aim a data set of 4741 water molecules abstracted from 179 high-resolution (≤ 2.30 Å) X-ray crystal structures of protein-protein complexes was analyzed with a suite of modeling tools based on HINT. The second aim is to observe the effect of adding interfacial water molecules in developing a model for the protein-protein interaction between pyridoxal kinase and serine hydroxymethyltransferase. This model was created to explore the possibility of the formation of a channel between the two proteins upon interaction providing a safe way to transport the substrate pyridoxal 5’-phosphate (active form of vitamin B6). This work demonstrates a substantial progress in the understanding of the role of water molecules in protein-protein binding.

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