This thesis project focused on using a sequence-based, high-performance computational tool to design synthetic proteins and is part of current collaborative research on Duchenne Muscular Dystrophy (DMD). A possible treatment for DMD consists of injecting patients with healthy muscle satellite cells grown in tissue culture. However, such cells cannot currently be produced in quantity because they convert to muscle cells (differentiate) prematurely. Using InSiPS, the In-Silico Protein Synthesizer, protein sequences were designed to interact with target proteins and inhibit the protein-protein interaction proposed to regulate the premature differentiation. The resulting sequences were predicted to interact with the target proteins with high specificity (99.98%). Complementary biochemistry experiments indicated interactions with the intended target for two out of ten synthetic proteins. These results are being studied as part of the ongoing research seeking to develop a treatment for DMD. I would like to acknowledge and give my sincerest appreciation to the person who made possible my participation in this research project, Dr. Frank Dehne. I will always be grateful for having such a recognized investigator as my thesis supervisor, who was always happy to help and give advice with his contagious passion for research that motivated me to improve myself. An enormous thank you to Dr. Andrew Schoenrock, for his infinite patience in helping me at every step of the project, and whose expertise and knowledge of PIPE and InSiPS were crucial for my progress. Also, a big thank to Daniel Burnside for kindly helping me to understand and to explain biochemistry concepts. I also thank Dr. Ashkan Golshani and everyone in the Carleton Bioinformatics group. I was very lucky to be among dedicated investigators who were always happy to provide ideas to improve the present work. Special thanks go to Dr. Alexandre Blais, who developed the initial research proposal, who designed the biochemical experimental validation and who led the group that performed it-all with great commitment and a high sense of collaboration. My infinite appreciation goes also to Carole Love, and all the hard-work she put into proofreading and helping me with suggestions that make me feel proud of my thesis writing. I want to express my deepest gratitude to the Mexican National Council for Science and Technology (CONACyT) for sponsoring my graduate studies on behalf of my country-México-and for helping me to pursue this major milestone in my life. I am very fortunate to have in my life a special colleague who happens to be my husband and love of my life. Thank you, Pablo for your unending support and for sharing with me this adventure.